Starting phenix.real_space_refine
on Thu Feb  5 23:07:48 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9hlx_52275/02_2026/9hlx_52275.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9hlx_52275/02_2026/9hlx_52275.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9hlx_52275/02_2026/9hlx_52275.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9hlx_52275/02_2026/9hlx_52275.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9hlx_52275/02_2026/9hlx_52275.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9hlx_52275/02_2026/9hlx_52275.cif"
  }
  resolution = 3.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.007
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      41      5.49       5
     S      22      5.16       5
     C    6372      2.51       5
     N    1780      2.21       5
     O    2071      1.98       5
     H    9966      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 51 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 20252
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 18950
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1156, 18950
          Classifications: {'peptide': 1156}
          Modifications used: {'NH3': 1}
          Link IDs: {'PTRANS': 22, 'TRANS': 1133}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 1302
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 41, 1302
          Classifications: {'RNA': 41}
          Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 13, 'rna3p_pur': 12, 'rna3p_pyr': 10}
          Link IDs: {'rna2p': 18, 'rna3p': 22}
  Time building chain proxies: 3.19, per 1000 atoms: 0.16
  Number of scatterers: 20252
  At special positions: 0
  Unit cell: (98.28, 108.29, 132.86, 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      22     16.00
     P      41     15.00
     O    2071      8.00
     N    1780      7.00
     C    6372      6.00
     H    9966      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.80
  Conformation dependent library (CDL) restraints added in 594.9 milliseconds
  

  2304 Ramachandran restraints generated.
    1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2206

  Finding SS restraints...
    Secondary structure from input PDB file:
      58 helices and 9 sheets defined
      58.0% alpha, 12.7% beta
      5 base pairs and 10 stacking pairs defined.
    Time for finding SS restraints: 3.34
  Creating SS restraints...
    Processing helix  chain 'A' and resid 21 through 29
      removed outlier: 4.226A  pdb=" N   ASP A  25 " --> pdb=" O   GLU A  21 " (cutoff:3.500A)
      removed outlier: 3.773A  pdb=" N   ILE A  26 " --> pdb=" O   ILE A  22 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 34 through 54
      removed outlier: 3.680A  pdb=" N   ARG A  50 " --> pdb=" O   LEU A  46 " (cutoff:3.500A)
      removed outlier: 4.174A  pdb=" N   ASN A  51 " --> pdb=" O   ASP A  47 " (cutoff:3.500A)
      removed outlier: 3.798A  pdb=" N   TYR A  52 " --> pdb=" O   GLN A  48 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 70 through 78
      removed outlier: 4.113A  pdb=" N   LEU A  74 " --> pdb=" O   LYS A  70 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 78 through 93
    Processing helix  chain 'A' and resid 105 through 109
    Processing helix  chain 'A' and resid 111 through 136
      removed outlier: 3.608A  pdb=" N   LYS A 115 " --> pdb=" O   GLY A 111 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 139 through 155
    Processing helix  chain 'A' and resid 159 through 169
      removed outlier: 3.552A  pdb=" N   LEU A 163 " --> pdb=" O   ALA A 159 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 178 through 202
      removed outlier: 3.511A  pdb=" N   GLN A 182 " --> pdb=" O   ASN A 178 " (cutoff:3.500A)
      removed outlier: 4.116A  pdb=" N   ILE A 188 " --> pdb=" O   LYS A 184 " (cutoff:3.500A)
      removed outlier: 4.033A  pdb=" N   LEU A 189 " --> pdb=" O   ASN A 185 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 217 through 222
      removed outlier: 4.223A  pdb=" N   ILE A 221 " --> pdb=" O   ASN A 217 " (cutoff:3.500A)
      removed outlier: 3.735A  pdb=" N   ASN A 222 " --> pdb=" O   TYR A 218 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 217 through 222'
    Processing helix  chain 'A' and resid 227 through 238
      removed outlier: 3.517A  pdb=" N   GLU A 231 " --> pdb=" O   ASP A 227 " (cutoff:3.500A)
      removed outlier: 3.949A  pdb=" N   ARG A 238 " --> pdb=" O   GLU A 234 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 242 through 250
      removed outlier: 4.323A  pdb=" N   PHE A 247 " --> pdb=" O   ASP A 244 " (cutoff:3.500A)
      removed outlier: 3.535A  pdb=" N   LEU A 249 " --> pdb=" O   ILE A 246 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 255 through 268
    Processing helix  chain 'A' and resid 281 through 285
    Processing helix  chain 'A' and resid 292 through 313
    Processing helix  chain 'A' and resid 316 through 323
    Processing helix  chain 'A' and resid 332 through 356
    Processing helix  chain 'A' and resid 358 through 384
    Processing helix  chain 'A' and resid 384 through 419
      removed outlier: 4.098A  pdb=" N   GLU A 400 " --> pdb=" O   THR A 396 " (cutoff:3.500A)
      removed outlier: 3.756A  pdb=" N   HIS A 401 " --> pdb=" O   ILE A 397 " (cutoff:3.500A)
      removed outlier: 3.549A  pdb=" N   GLY A 402 " --> pdb=" O   SER A 398 " (cutoff:3.500A)
      removed outlier: 3.591A  pdb=" N   LEU A 407 " --> pdb=" O   LYS A 403 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 443 through 453
      removed outlier: 3.861A  pdb=" N   SER A 453 " --> pdb=" O   GLN A 449 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 471 through 481
    Processing helix  chain 'A' and resid 482 through 486
      removed outlier: 3.659A  pdb=" N   ASN A 485 " --> pdb=" O   PHE A 482 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 488 through 494
      removed outlier: 3.512A  pdb=" N   ASN A 493 " --> pdb=" O   LYS A 489 " (cutoff:3.500A)
      removed outlier: 3.659A  pdb=" N   ILE A 494 " --> pdb=" O   PHE A 490 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 495 through 498
    Processing helix  chain 'A' and resid 509 through 514
    Processing helix  chain 'A' and resid 516 through 530
      removed outlier: 3.674A  pdb=" N   LYS A 522 " --> pdb=" O   GLN A 518 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 530 through 537
      removed outlier: 3.563A  pdb=" N   VAL A 536 " --> pdb=" O   TYR A 532 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 540 through 548
      removed outlier: 4.043A  pdb=" N   ALA A 546 " --> pdb=" O   GLN A 542 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 555 through 567
      removed outlier: 3.678A  pdb=" N   PHE A 559 " --> pdb=" O   SER A 555 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 577 through 587
      removed outlier: 3.514A  pdb=" N   LEU A 583 " --> pdb=" O   GLU A 579 " (cutoff:3.500A)
      removed outlier: 3.704A  pdb=" N   LYS A 587 " --> pdb=" O   LEU A 583 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 607 through 618
      removed outlier: 3.671A  pdb=" N   ILE A 612 " --> pdb=" O   SER A 608 " (cutoff:3.500A)
      removed outlier: 3.724A  pdb=" N   TRP A 617 " --> pdb=" O   TRP A 613 " (cutoff:3.500A)
      removed outlier: 3.610A  pdb=" N   THR A 618 " --> pdb=" O   LYS A 614 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 618 through 624
      removed outlier: 3.869A  pdb=" N   LYS A 622 " --> pdb=" O   THR A 618 " (cutoff:3.500A)
      removed outlier: 3.871A  pdb=" N   GLN A 623 " --> pdb=" O   SER A 619 " (cutoff:3.500A)
      removed outlier: 3.767A  pdb=" N   ASN A 624 " --> pdb=" O   GLU A 620 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 618 through 624'
    Processing helix  chain 'A' and resid 685 through 698
    Processing helix  chain 'A' and resid 699 through 700
      No H-bonds generated for 'chain 'A' and resid 699 through 700'
    Processing helix  chain 'A' and resid 701 through 703
      No H-bonds generated for 'chain 'A' and resid 701 through 703'
    Processing helix  chain 'A' and resid 725 through 729
    Processing helix  chain 'A' and resid 732 through 741
    Processing helix  chain 'A' and resid 742 through 747
      removed outlier: 3.545A  pdb=" N   TYR A 746 " --> pdb=" O   LYS A 742 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 771 through 773
      No H-bonds generated for 'chain 'A' and resid 771 through 773'
    Processing helix  chain 'A' and resid 774 through 779
    Processing helix  chain 'A' and resid 779 through 788
    Processing helix  chain 'A' and resid 790 through 801
    Processing helix  chain 'A' and resid 828 through 849
    Processing helix  chain 'A' and resid 869 through 878
    Processing helix  chain 'A' and resid 879 through 884
    Processing helix  chain 'A' and resid 887 through 900
    Processing helix  chain 'A' and resid 908 through 917
      removed outlier: 3.687A  pdb=" N   ARG A 917 " --> pdb=" O   LYS A 913 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 948 through 951
      removed outlier: 4.446A  pdb=" N   PHE A 951 " --> pdb=" O   THR A 948 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 948 through 951'
    Processing helix  chain 'A' and resid 968 through 982
      removed outlier: 3.624A  pdb=" N   LYS A 973 " --> pdb=" O   GLU A 969 " (cutoff:3.500A)
      removed outlier: 3.723A  pdb=" N   ASN A 980 " --> pdb=" O   ILE A 976 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 989 through 1024
      removed outlier: 4.476A  pdb=" N   LEU A 995 " --> pdb=" O   GLU A 991 " (cutoff:3.500A)
      removed outlier: 3.612A  pdb=" N   THR A1000 " --> pdb=" O   LYS A 996 " (cutoff:3.500A)
      removed outlier: 3.939A  pdb=" N   ALA A1006 " --> pdb=" O   LYS A1002 " (cutoff:3.500A)
      removed outlier: 4.120A  pdb=" N   ASN A1007 " --> pdb=" O   ALA A1003 " (cutoff:3.500A)
      removed outlier: 3.844A  pdb=" N   ALA A1008 " --> pdb=" O   LEU A1004 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1041 through 1047
      removed outlier: 3.699A  pdb=" N   GLU A1044 " --> pdb=" O   ASP A1041 " (cutoff:3.500A)
      removed outlier: 3.624A  pdb=" N   PHE A1046 " --> pdb=" O   ILE A1043 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1049 through 1063
      removed outlier: 3.706A  pdb=" N   ILE A1053 " --> pdb=" O   ASN A1049 " (cutoff:3.500A)
      removed outlier: 3.523A  pdb=" N   TYR A1059 " --> pdb=" O   GLU A1055 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1064 through 1066
      No H-bonds generated for 'chain 'A' and resid 1064 through 1066'
    Processing helix  chain 'A' and resid 1073 through 1077
      removed outlier: 3.615A  pdb=" N   ALA A1076 " --> pdb=" O   SER A1073 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1078 through 1083
      removed outlier: 4.419A  pdb=" N   GLY A1081 " --> pdb=" O   ARG A1078 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   ILE A1082 " --> pdb=" O   ALA A1079 " (cutoff:3.500A)
      removed outlier: 3.657A  pdb=" N   GLU A1083 " --> pdb=" O   ASN A1080 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 1078 through 1083'
    Processing helix  chain 'A' and resid 1135 through 1137
      No H-bonds generated for 'chain 'A' and resid 1135 through 1137'
    Processing helix  chain 'A' and resid 1138 through 1156
      removed outlier: 3.613A  pdb=" N   PHE A1142 " --> pdb=" O   GLY A1138 " (cutoff:3.500A)
      removed outlier: 3.688A  pdb=" N   LYS A1156 " --> pdb=" O   PHE A1152 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1157 through 1159
      No H-bonds generated for 'chain 'A' and resid 1157 through 1159'
    Processing sheet with id=AA1, first strand: chain 'A' and resid 568 through 573
      removed outlier: 3.539A  pdb=" N   GLU A 468 " --> pdb=" O   ARG A 569 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   TRP A 466 " --> pdb=" O   PHE A 571 " (cutoff:3.500A)
      removed outlier: 3.588A  pdb=" N   ILE A 427 " --> pdb=" O   PHE A 465 " (cutoff:3.500A)
      removed outlier: 5.839A  pdb=" N   PHE A 467 " --> pdb=" O   ALA A 425 " (cutoff:3.500A)
      removed outlier: 8.798A  pdb=" N   ALA A 425 " --> pdb=" O   PHE A 467 " (cutoff:3.500A)
      removed outlier: 13.990A  pdb=" N   SER A 469 " --> pdb=" O   TYR A 423 " (cutoff:3.500A)
      removed outlier: 16.792A  pdb=" N   TYR A 423 " --> pdb=" O   SER A 469 " (cutoff:3.500A)
      removed outlier: 13.904A  pdb=" N   LEU A 421 " --> pdb=" O   LEU A 209 " (cutoff:3.500A)
      removed outlier: 12.508A  pdb=" N   VAL A 211 " --> pdb=" O   LEU A 421 " (cutoff:3.500A)
      removed outlier: 9.216A  pdb=" N   TYR A 423 " --> pdb=" O   VAL A 211 " (cutoff:3.500A)
      removed outlier: 7.000A  pdb=" N   LYS A 213 " --> pdb=" O   TYR A 423 " (cutoff:3.500A)
      removed outlier: 7.826A  pdb=" N   ALA A 425 " --> pdb=" O   LYS A 213 " (cutoff:3.500A)
      removed outlier: 6.841A  pdb=" N   SER A 215 " --> pdb=" O   ALA A 425 " (cutoff:3.500A)
      removed outlier: 9.091A  pdb=" N   ILE A 427 " --> pdb=" O   SER A 215 " (cutoff:3.500A)
      removed outlier: 6.106A  pdb=" N   TYR A 638 " --> pdb=" O   PRO A 210 " (cutoff:3.500A)
      removed outlier: 4.005A  pdb=" N   ALA A 212 " --> pdb=" O   ILE A 636 " (cutoff:3.500A)
      removed outlier: 6.981A  pdb=" N   GLU A 633 " --> pdb=" O   THR A 669 " (cutoff:3.500A)
      removed outlier: 5.019A  pdb=" N   THR A 669 " --> pdb=" O   GLU A 633 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 568 through 573
      removed outlier: 3.539A  pdb=" N   GLU A 468 " --> pdb=" O   ARG A 569 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   TRP A 466 " --> pdb=" O   PHE A 571 " (cutoff:3.500A)
      removed outlier: 3.588A  pdb=" N   ILE A 427 " --> pdb=" O   PHE A 465 " (cutoff:3.500A)
      removed outlier: 5.839A  pdb=" N   PHE A 467 " --> pdb=" O   ALA A 425 " (cutoff:3.500A)
      removed outlier: 8.798A  pdb=" N   ALA A 425 " --> pdb=" O   PHE A 467 " (cutoff:3.500A)
      removed outlier: 13.990A  pdb=" N   SER A 469 " --> pdb=" O   TYR A 423 " (cutoff:3.500A)
      removed outlier: 16.792A  pdb=" N   TYR A 423 " --> pdb=" O   SER A 469 " (cutoff:3.500A)
      removed outlier: 5.453A  pdb=" N   HIS A 434 " --> pdb=" O   ILE A 593 " (cutoff:3.500A)
      removed outlier: 3.601A  pdb=" N   ILE A 593 " --> pdb=" O   HIS A 434 " (cutoff:3.500A)
      removed outlier: 7.107A  pdb=" N   ILE A 590 " --> pdb=" O   GLN A  17 " (cutoff:3.500A)
      removed outlier: 3.659A  pdb=" N   GLN A  17 " --> pdb=" O   ILE A 590 " (cutoff:3.500A)
      removed outlier: 3.632A  pdb=" N   LYS A  13 " --> pdb=" O   THR A 594 " (cutoff:3.500A)
      removed outlier: 3.622A  pdb=" N   VAL A   6 " --> pdb=" O   GLU A 672 " (cutoff:3.500A)
      removed outlier: 4.000A  pdb=" N   TYR A 664 " --> pdb=" O   LEU A  14 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 68 through 69
    Processing sheet with id=AA4, first strand: chain 'A' and resid 275 through 277
    Processing sheet with id=AA5, first strand: chain 'A' and resid 809 through 810
      removed outlier: 6.949A  pdb=" N   GLU A1026 " --> pdb=" O   ILE A 705 " (cutoff:3.500A)
      removed outlier: 4.460A  pdb=" N   PHE A 707 " --> pdb=" O   GLU A1026 " (cutoff:3.500A)
      removed outlier: 3.592A  pdb=" N   GLU A1032 " --> pdb=" O   ILE A 711 " (cutoff:3.500A)
      removed outlier: 8.078A  pdb=" N   GLY A1096 " --> pdb=" O   GLY A1027 " (cutoff:3.500A)
      removed outlier: 6.346A  pdb=" N   ILE A1029 " --> pdb=" O   GLY A1096 " (cutoff:3.500A)
      removed outlier: 7.742A  pdb=" N   ILE A1098 " --> pdb=" O   ILE A1029 " (cutoff:3.500A)
      removed outlier: 6.639A  pdb=" N   LYS A1031 " --> pdb=" O   ILE A1098 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 748 through 753
    Processing sheet with id=AA7, first strand: chain 'A' and resid 759 through 761
    Processing sheet with id=AA8, first strand: chain 'A' and resid 816 through 818
    Processing sheet with id=AA9, first strand: chain 'A' and resid 933 through 935

    482 hydrogen bonds defined for protein.
    1356 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      12 hydrogen bonds
      24 hydrogen bond angles
      0 basepair planarities
      5 basepair parallelities
      10 stacking parallelities
  Total time for adding SS restraints: 4.89

  Time building geometry restraints manager: 2.46 seconds

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

  Histogram of bond lengths:
        0.84 -     1.03: 5079
        1.03 -     1.23: 5089
        1.23 -     1.42: 5184
        1.42 -     1.62: 5125
        1.62 -     1.81: 34
  Bond restraints: 20511
  Sorted by residual:
  bond pdb=" CE1 HIS A 434 "
       pdb=" NE2 HIS A 434 "
    ideal  model  delta    sigma   weight residual
    1.321  1.232  0.089 1.00e-02 1.00e+04 7.99e+01
  bond pdb=" CE1 HIS A 401 "
       pdb=" NE2 HIS A 401 "
    ideal  model  delta    sigma   weight residual
    1.321  1.232  0.089 1.00e-02 1.00e+04 7.93e+01
  bond pdb=" CE1 HIS A 986 "
       pdb=" NE2 HIS A 986 "
    ideal  model  delta    sigma   weight residual
    1.321  1.232  0.089 1.00e-02 1.00e+04 7.89e+01
  bond pdb=" CE1 HIS A  77 "
       pdb=" NE2 HIS A  77 "
    ideal  model  delta    sigma   weight residual
    1.321  1.233  0.088 1.00e-02 1.00e+04 7.82e+01
  bond pdb=" CE1 HIS A 609 "
       pdb=" NE2 HIS A 609 "
    ideal  model  delta    sigma   weight residual
    1.321  1.233  0.088 1.00e-02 1.00e+04 7.76e+01
  ... (remaining 20506 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.60: 27242
        2.60 -     5.21: 6439
        5.21 -     7.81: 2846
        7.81 -    10.41: 486
       10.41 -    13.01: 84
  Bond angle restraints: 37097
  Sorted by residual:
  angle pdb=" CA  PHE A 844 "
        pdb=" CB  PHE A 844 "
        pdb=" CG  PHE A 844 "
      ideal   model   delta    sigma   weight residual
     113.80  121.58   -7.78 1.00e+00 1.00e+00 6.05e+01
  angle pdb=" C   ARG A1131 "
        pdb=" N   ILE A1132 "
        pdb=" CA  ILE A1132 "
      ideal   model   delta    sigma   weight residual
     122.97  130.21   -7.24 9.80e-01 1.04e+00 5.46e+01
  angle pdb=" CA  ASN A 833 "
        pdb=" CB  ASN A 833 "
        pdb=" CG  ASN A 833 "
      ideal   model   delta    sigma   weight residual
     112.60  119.89   -7.29 1.00e+00 1.00e+00 5.32e+01
  angle pdb=" CA  ASP A 865 "
        pdb=" CB  ASP A 865 "
        pdb=" CG  ASP A 865 "
      ideal   model   delta    sigma   weight residual
     112.60  119.82   -7.22 1.00e+00 1.00e+00 5.22e+01
  angle pdb=" CA  ASP A 901 "
        pdb=" CB  ASP A 901 "
        pdb=" CG  ASP A 901 "
      ideal   model   delta    sigma   weight residual
     112.60  119.80   -7.20 1.00e+00 1.00e+00 5.18e+01
  ... (remaining 37092 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.53: 9267
       35.53 -    71.06: 271
       71.06 -   106.59: 48
      106.59 -   142.12: 2
      142.12 -   177.65: 6
  Dihedral angle restraints: 9594
    sinusoidal: 5605
      harmonic: 3989
  Sorted by residual:
  dihedral pdb=" O4'   U B  49 "
           pdb=" C1'   U B  49 "
           pdb=" N1    U B  49 "
           pdb=" C2    U B  49 "
      ideal   model   delta sinusoidal    sigma   weight residual
     232.00   55.58  176.42     1      1.70e+01 3.46e-03 6.64e+01
  dihedral pdb=" O4'   C B  13 "
           pdb=" C1'   C B  13 "
           pdb=" N1    C B  13 "
           pdb=" C2    C B  13 "
      ideal   model   delta sinusoidal    sigma   weight residual
     232.00   67.61  164.39     1      1.70e+01 3.46e-03 6.52e+01
  dihedral pdb=" O4'   U B  43 "
           pdb=" C1'   U B  43 "
           pdb=" N1    U B  43 "
           pdb=" C2    U B  43 "
      ideal   model   delta sinusoidal    sigma   weight residual
     232.00   68.99  163.01     1      1.70e+01 3.46e-03 6.50e+01
  ... (remaining 9591 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.149: 935
       0.149 -    0.299: 46
       0.299 -    0.448: 113
       0.448 -    0.597: 406
       0.597 -    0.746: 113
  Chirality restraints: 1613
  Sorted by residual:
  chirality pdb=" CG  LEU A 778 "
            pdb=" CB  LEU A 778 "
            pdb=" CD1 LEU A 778 "
            pdb=" CD2 LEU A 778 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -1.84   -0.75 2.00e-01 2.50e+01 1.39e+01
  chirality pdb=" CG  LEU A 475 "
            pdb=" CB  LEU A 475 "
            pdb=" CD1 LEU A 475 "
            pdb=" CD2 LEU A 475 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -1.85   -0.74 2.00e-01 2.50e+01 1.38e+01
  chirality pdb=" CG  LEU A 408 "
            pdb=" CB  LEU A 408 "
            pdb=" CD1 LEU A 408 "
            pdb=" CD2 LEU A 408 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -1.86   -0.73 2.00e-01 2.50e+01 1.33e+01
  ... (remaining 1610 not shown)

  Planarity restraints: 2862
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   C B  26 "   -0.304 2.00e-02 2.50e+03   1.22e-01 4.07e+02
        pdb=" N1    C B  26 "    0.055 2.00e-02 2.50e+03
        pdb=" C2    C B  26 "    0.048 2.00e-02 2.50e+03
        pdb=" O2    C B  26 "    0.174 2.00e-02 2.50e+03
        pdb=" N3    C B  26 "   -0.023 2.00e-02 2.50e+03
        pdb=" C4    C B  26 "   -0.064 2.00e-02 2.50e+03
        pdb=" N4    C B  26 "   -0.113 2.00e-02 2.50e+03
        pdb=" C5    C B  26 "    0.024 2.00e-02 2.50e+03
        pdb=" C6    C B  26 "    0.076 2.00e-02 2.50e+03
        pdb=" H5    C B  26 "    0.026 2.00e-02 2.50e+03
        pdb=" H6    C B  26 "    0.100 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   G B  37 "    0.254 2.00e-02 2.50e+03   9.94e-02 3.46e+02
        pdb=" N9    G B  37 "   -0.027 2.00e-02 2.50e+03
        pdb=" C8    G B  37 "   -0.069 2.00e-02 2.50e+03
        pdb=" N7    G B  37 "   -0.064 2.00e-02 2.50e+03
        pdb=" C5    G B  37 "   -0.030 2.00e-02 2.50e+03
        pdb=" C6    G B  37 "    0.020 2.00e-02 2.50e+03
        pdb=" O6    G B  37 "    0.062 2.00e-02 2.50e+03
        pdb=" N1    G B  37 "    0.022 2.00e-02 2.50e+03
        pdb=" C2    G B  37 "   -0.028 2.00e-02 2.50e+03
        pdb=" N2    G B  37 "   -0.164 2.00e-02 2.50e+03
        pdb=" N3    G B  37 "   -0.037 2.00e-02 2.50e+03
        pdb=" C4    G B  37 "   -0.036 2.00e-02 2.50e+03
        pdb=" H8    G B  37 "   -0.060 2.00e-02 2.50e+03
        pdb=" H1    G B  37 "    0.157 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   U B  27 "    0.172 2.00e-02 2.50e+03   1.03e-01 3.19e+02
        pdb=" N1    U B  27 "    0.022 2.00e-02 2.50e+03
        pdb=" C2    U B  27 "    0.062 2.00e-02 2.50e+03
        pdb=" O2    U B  27 "   -0.109 2.00e-02 2.50e+03
        pdb=" N3    U B  27 "    0.065 2.00e-02 2.50e+03
        pdb=" C4    U B  27 "    0.081 2.00e-02 2.50e+03
        pdb=" O4    U B  27 "    0.125 2.00e-02 2.50e+03
        pdb=" C5    U B  27 "   -0.011 2.00e-02 2.50e+03
        pdb=" C6    U B  27 "   -0.058 2.00e-02 2.50e+03
        pdb=" H5    U B  27 "   -0.035 2.00e-02 2.50e+03
        pdb=" H3    U B  27 "   -0.182 2.00e-02 2.50e+03
        pdb=" H6    U B  27 "   -0.133 2.00e-02 2.50e+03
  ... (remaining 2859 not shown)

  Histogram of nonbonded interaction distances:
        1.44 -     2.08: 421
        2.08 -     2.71: 30421
        2.71 -     3.34: 55811
        3.34 -     3.97: 66249
        3.97 -     4.60: 103726
  Nonbonded interactions: 256628
  Sorted by model distance:
  nonbonded pdb=" O   ARG A 983 "
            pdb="HH11 ARG A 983 "
     model   vdw
     1.444 2.450
  nonbonded pdb=" OD2 ASP A 597 "
            pdb=" HG1 THR A 610 "
     model   vdw
     1.544 2.450
  nonbonded pdb=" OE1 GLU A  81 "
            pdb=" H   GLU A  81 "
     model   vdw
     1.557 2.450
  nonbonded pdb=" OE1 GLU A 517 "
            pdb=" H   LEU A 556 "
     model   vdw
     1.566 2.450
  nonbonded pdb=" HZ3 LYS A1001 "
            pdb=" O   SER A1047 "
     model   vdw
     1.566 2.450
  ... (remaining 256623 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:             1.580
  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:             0.070
  Extract box with map and model:          0.190
  Check model and map are aligned:         0.040
  Set scattering table:                    0.030
  Process input model:                     21.310
  Find NCS groups from input model:        0.070
  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:1.410
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   24.730
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6156
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      :  0.037   0.146  10545  Z= 1.936
  Angle     :  2.815  12.660  14364  Z= 1.785
  Chirality :  0.345   0.746   1613
  Planarity :  0.011   0.139   1702
  Dihedral  : 17.659 177.645   4306
  Min Nonbonded Distance : 2.063

Molprobity Statistics.
  All-atom Clashscore : 2.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.56 %
    Favored  : 94.44 %
  Rotamer:
    Outliers :  0.96 %
    Allowed  :  6.07 %
    Favored  : 92.97 %
  Cbeta Deviations : 22.94 %
  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 are not related in a simple way.
  whole: -0.44 (0.24), residues: 1152
  helix:  0.33 (0.22), residues: 532
  sheet:  1.24 (0.56), residues: 86
  loop : -1.17 (0.25), residues: 534

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 639 
 TYR   0.088   0.012   TYR A 472 
 PHE   0.076   0.009   PHE A 935 
 TRP   0.040   0.006   TRP A 835 
 HIS   0.011   0.001   HIS A  98 

Details of bonding type rmsd
  covalent geometry    : bond        0.03739 (10545)
  covalent geometry    : angle       2.81496 (14364)
  hydrogen bonds       : bond        0.18757 (  485)
  hydrogen bonds       : angle       6.25544 ( 1380)

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

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

  2304 Ramachandran restraints generated.
    1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2304 Ramachandran restraints generated.
    1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  199 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 189
  time to evaluate  : 0.474 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   18 ASN cc_start: 0.7901 (t0) cc_final: 0.7525 (m-40)
REVERT: A   30 GLN cc_start: 0.8228 (mt0) cc_final: 0.7985 (mt0)
REVERT: A   47 ASP cc_start: 0.8417 (t70) cc_final: 0.8051 (t0)
REVERT: A   72 GLU cc_start: 0.6828 (tm-30) cc_final: 0.6555 (tm-30)
REVERT: A  178 ASN cc_start: 0.7183 (p0) cc_final: 0.6815 (p0)
REVERT: A  479 CYS cc_start: 0.8060 (t) cc_final: 0.7711 (m)
REVERT: A  545 GLN cc_start: 0.8366 (tp40) cc_final: 0.7993 (tp-100)
REVERT: A  627 GLU cc_start: 0.7389 (tp30) cc_final: 0.6673 (tt0)
REVERT: A  679 LYS cc_start: 0.6936 (tptm) cc_final: 0.6666 (ttpt)
REVERT: A  893 LYS cc_start: 0.8593 (mttt) cc_final: 0.8231 (tttt)
REVERT: A  970 GLU cc_start: 0.7720 (mm-30) cc_final: 0.7250 (tp30)
REVERT: A 1124 LYS cc_start: 0.8708 (mmmt) cc_final: 0.8184 (mtpp)
  outliers start: 10
  outliers final: 2
  residues processed: 192
  average time/residue: 0.2470
  time to fit residues: 63.6948
Evaluate side-chains
  126 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 124
  time to evaluate  : 0.559 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  604 ASP
Chi-restraints excluded: chain A residue  880 GLU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 108 optimal weight:    0.8980
   chunk 49 optimal weight:    1.9990
   chunk 97 optimal weight:    0.9990
   chunk 113 optimal weight:    0.9980
   chunk 53 optimal weight:    2.9990
   chunk 5 optimal weight:    0.9990
   chunk 33 optimal weight:   10.0000
   chunk 65 optimal weight:    0.9990
   chunk 62 optimal weight:    0.9980
   chunk 51 optimal weight:    2.9990
   chunk 117 optimal weight:    0.8980
   overall best weight:    0.9582

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

Flipped N/Q/H residues before XYZ refinement:
A 103 GLN
A 788 ASN
A 945 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4159 r_free = 0.4159 target = 0.187698 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3629 r_free = 0.3629 target = 0.139155 restraints weight = 41569.853|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3608 r_free = 0.3608 target = 0.139616 restraints weight = 29245.662|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3631 r_free = 0.3631 target = 0.142246 restraints weight = 22817.099|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3636 r_free = 0.3636 target = 0.142699 restraints weight = 16714.783|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3640 r_free = 0.3640 target = 0.143254 restraints weight = 15411.834|
|-----------------------------------------------------------------------------|
r_work (final): 0.3602
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7693
moved from start:          0.2111

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024  10545  Z= 0.131
  Angle     :  0.582   7.717  14364  Z= 0.318
  Chirality :  0.038   0.175   1613
  Planarity :  0.003   0.035   1702
  Dihedral  : 18.652 175.418   1871
  Min Nonbonded Distance : 2.330

Molprobity Statistics.
  All-atom Clashscore : 2.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.51 %
    Favored  : 95.49 %
  Rotamer:
    Outliers :  1.35 %
    Allowed  :  8.57 %
    Favored  : 90.08 %
  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 are not related in a simple way.
  whole:  1.19 (0.25), residues: 1152
  helix:  2.23 (0.22), residues: 545
  sheet:  0.86 (0.50), residues: 106
  loop : -0.89 (0.28), residues: 501

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 639 
 TYR   0.018   0.001   TYR A 339 
 PHE   0.019   0.001   PHE A 939 
 TRP   0.011   0.001   TRP A 466 
 HIS   0.007   0.001   HIS A  98 

Details of bonding type rmsd
  covalent geometry    : bond        0.00268 (10545)
  covalent geometry    : angle       0.58178 (14364)
  hydrogen bonds       : bond        0.04597 (  485)
  hydrogen bonds       : angle       4.74014 ( 1380)

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

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

  2304 Ramachandran restraints generated.
    1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2304 Ramachandran restraints generated.
    1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 132
  time to evaluate  : 0.512 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   47 ASP cc_start: 0.8635 (t70) cc_final: 0.8108 (t0)
REVERT: A   72 GLU cc_start: 0.7665 (tm-30) cc_final: 0.7355 (tm-30)
REVERT: A  178 ASN cc_start: 0.9035 (p0) cc_final: 0.8741 (p0)
REVERT: A  387 TRP cc_start: 0.9124 (t-100) cc_final: 0.8862 (t-100)
REVERT: A  797 MET cc_start: 0.8544 (tmm) cc_final: 0.8260 (tmm)
REVERT: A  845 GLU cc_start: 0.8025 (tp30) cc_final: 0.7736 (tp30)
REVERT: A  979 TYR cc_start: 0.6052 (m-80) cc_final: 0.4330 (m-80)
REVERT: A 1124 LYS cc_start: 0.8633 (mmmt) cc_final: 0.8156 (mtpp)
  outliers start: 14
  outliers final: 9
  residues processed: 141
  average time/residue: 0.2041
  time to fit residues: 41.3110
Evaluate side-chains
  117 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 108
  time to evaluate  : 0.565 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 LEU
Chi-restraints excluded: chain A residue  198 VAL
Chi-restraints excluded: chain A residue  260 GLU
Chi-restraints excluded: chain A residue  454 LEU
Chi-restraints excluded: chain A residue  606 ILE
Chi-restraints excluded: chain A residue  680 ILE
Chi-restraints excluded: chain A residue  808 LEU
Chi-restraints excluded: chain A residue  934 LEU
Chi-restraints excluded: chain A residue 1109 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 1 optimal weight:    1.9990
   chunk 75 optimal weight:    5.9990
   chunk 3 optimal weight:    1.9990
   chunk 94 optimal weight:    0.9990
   chunk 60 optimal weight:    0.4980
   chunk 43 optimal weight:    0.2980
   chunk 6 optimal weight:    3.9990
   chunk 81 optimal weight:    0.6980
   chunk 51 optimal weight:    6.9990
   chunk 118 optimal weight:    9.9990
   chunk 5 optimal weight:    4.9990
   overall best weight:    0.8984

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4253 r_free = 0.4253 target = 0.197377 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3724 r_free = 0.3724 target = 0.147574 restraints weight = 41629.881|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3709 r_free = 0.3709 target = 0.149125 restraints weight = 27966.119|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3735 r_free = 0.3735 target = 0.151947 restraints weight = 23041.712|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3738 r_free = 0.3738 target = 0.152423 restraints weight = 15613.257|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3745 r_free = 0.3745 target = 0.153135 restraints weight = 14883.122|
|-----------------------------------------------------------------------------|
r_work (final): 0.3717
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7724
moved from start:          0.2690

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027  10545  Z= 0.110
  Angle     :  0.493   5.181  14364  Z= 0.274
  Chirality :  0.036   0.167   1613
  Planarity :  0.003   0.042   1702
  Dihedral  : 18.545 174.103   1866
  Min Nonbonded Distance : 2.307

Molprobity Statistics.
  All-atom Clashscore : 2.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.60 %
    Favored  : 95.40 %
  Rotamer:
    Outliers :  1.16 %
    Allowed  :  9.34 %
    Favored  : 89.50 %
  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 are not related in a simple way.
  whole:  1.64 (0.26), residues: 1152
  helix:  2.72 (0.23), residues: 544
  sheet:  0.86 (0.49), residues: 116
  loop : -0.79 (0.29), residues: 492

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 954 
 TYR   0.010   0.001   TYR A 659 
 PHE   0.018   0.001   PHE A 307 
 TRP   0.011   0.001   TRP A 466 
 HIS   0.006   0.001   HIS A 986 

Details of bonding type rmsd
  covalent geometry    : bond        0.00232 (10545)
  covalent geometry    : angle       0.49272 (14364)
  hydrogen bonds       : bond        0.03814 (  485)
  hydrogen bonds       : angle       4.27614 ( 1380)

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

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

  2304 Ramachandran restraints generated.
    1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2304 Ramachandran restraints generated.
    1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 112
  time to evaluate  : 0.431 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   18 ASN cc_start: 0.8303 (t0) cc_final: 0.7880 (t0)
REVERT: A   47 ASP cc_start: 0.8620 (t70) cc_final: 0.8024 (t0)
REVERT: A  387 TRP cc_start: 0.9119 (t-100) cc_final: 0.8827 (t-100)
REVERT: A  797 MET cc_start: 0.8523 (tmm) cc_final: 0.8275 (tmm)
REVERT: A  845 GLU cc_start: 0.7929 (tp30) cc_final: 0.7617 (tp30)
REVERT: A  979 TYR cc_start: 0.6077 (m-80) cc_final: 0.5568 (m-80)
REVERT: A  987 ASP cc_start: 0.6370 (t0) cc_final: 0.6130 (t0)
REVERT: A 1124 LYS cc_start: 0.8582 (mmmt) cc_final: 0.8149 (mtpp)
  outliers start: 12
  outliers final: 8
  residues processed: 122
  average time/residue: 0.2002
  time to fit residues: 35.3365
Evaluate side-chains
  112 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 104
  time to evaluate  : 0.531 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 LEU
Chi-restraints excluded: chain A residue   95 LEU
Chi-restraints excluded: chain A residue  198 VAL
Chi-restraints excluded: chain A residue  454 LEU
Chi-restraints excluded: chain A residue  606 ILE
Chi-restraints excluded: chain A residue  680 ILE
Chi-restraints excluded: chain A residue  934 LEU
Chi-restraints excluded: chain A residue 1073 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 113 optimal weight:    4.9990
   chunk 62 optimal weight:    2.9990
   chunk 15 optimal weight:    2.9990
   chunk 19 optimal weight:    0.9980
   chunk 22 optimal weight:    1.9990
   chunk 118 optimal weight:   10.0000
   chunk 64 optimal weight:    0.7980
   chunk 20 optimal weight:    0.9990
   chunk 41 optimal weight:    0.9990
   chunk 67 optimal weight:    2.9990
   chunk 60 optimal weight:    0.9980
   overall best weight:    0.9584

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

Flipped N/Q/H residues before XYZ refinement:
A 476 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4243 r_free = 0.4243 target = 0.196450 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3708 r_free = 0.3708 target = 0.145797 restraints weight = 41478.408|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3694 r_free = 0.3694 target = 0.146804 restraints weight = 27689.753|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3717 r_free = 0.3717 target = 0.149423 restraints weight = 24094.424|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3724 r_free = 0.3724 target = 0.150245 restraints weight = 16966.738|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3730 r_free = 0.3730 target = 0.150873 restraints weight = 15777.141|
|-----------------------------------------------------------------------------|
r_work (final): 0.3643
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7689
moved from start:          0.2978

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028  10545  Z= 0.106
  Angle     :  0.460   4.828  14364  Z= 0.255
  Chirality :  0.035   0.167   1613
  Planarity :  0.003   0.043   1702
  Dihedral  : 18.402 175.302   1866
  Min Nonbonded Distance : 2.350

Molprobity Statistics.
  All-atom Clashscore : 2.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.86 %
    Favored  : 95.14 %
  Rotamer:
    Outliers :  0.87 %
    Allowed  :  9.25 %
    Favored  : 89.88 %
  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 are not related in a simple way.
  whole:  1.76 (0.26), residues: 1152
  helix:  2.82 (0.23), residues: 548
  sheet:  0.85 (0.50), residues: 116
  loop : -0.76 (0.29), residues: 488

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 768 
 TYR   0.009   0.001   TYR A 659 
 PHE   0.021   0.001   PHE A 939 
 TRP   0.011   0.001   TRP A 466 
 HIS   0.003   0.001   HIS A  98 

Details of bonding type rmsd
  covalent geometry    : bond        0.00233 (10545)
  covalent geometry    : angle       0.45956 (14364)
  hydrogen bonds       : bond        0.03520 (  485)
  hydrogen bonds       : angle       4.03765 ( 1380)

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

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

  2304 Ramachandran restraints generated.
    1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2304 Ramachandran restraints generated.
    1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 112
  time to evaluate  : 0.529 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   18 ASN cc_start: 0.8346 (t0) cc_final: 0.8009 (m-40)
REVERT: A  797 MET cc_start: 0.8538 (tmm) cc_final: 0.8099 (tmm)
REVERT: A  845 GLU cc_start: 0.8004 (tp30) cc_final: 0.7764 (tp30)
REVERT: A  987 ASP cc_start: 0.6508 (t0) cc_final: 0.6302 (t0)
REVERT: A 1124 LYS cc_start: 0.8645 (mmmt) cc_final: 0.8175 (mtpp)
  outliers start: 9
  outliers final: 8
  residues processed: 119
  average time/residue: 0.2411
  time to fit residues: 39.8774
Evaluate side-chains
  107 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 99
  time to evaluate  : 0.518 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 LEU
Chi-restraints excluded: chain A residue  198 VAL
Chi-restraints excluded: chain A residue  454 LEU
Chi-restraints excluded: chain A residue  606 ILE
Chi-restraints excluded: chain A residue  680 ILE
Chi-restraints excluded: chain A residue  808 LEU
Chi-restraints excluded: chain A residue  934 LEU
Chi-restraints excluded: chain A residue 1073 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 15 optimal weight:    2.9990
   chunk 97 optimal weight:    3.9990
   chunk 51 optimal weight:    6.9990
   chunk 47 optimal weight:    2.9990
   chunk 114 optimal weight:    1.9990
   chunk 24 optimal weight:    5.9990
   chunk 20 optimal weight:    3.9990
   chunk 54 optimal weight:    0.0980
   chunk 3 optimal weight:    0.9980
   chunk 28 optimal weight:    0.0060
   chunk 45 optimal weight:    0.2980
   overall best weight:    0.6798

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

Flipped N/Q/H residues before XYZ refinement:
A  18 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4249 r_free = 0.4249 target = 0.197233 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3724 r_free = 0.3724 target = 0.147084 restraints weight = 41275.740|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3726 r_free = 0.3726 target = 0.150214 restraints weight = 27343.171|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3746 r_free = 0.3746 target = 0.152338 restraints weight = 21482.692|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3752 r_free = 0.3752 target = 0.153029 restraints weight = 15053.042|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3758 r_free = 0.3758 target = 0.153636 restraints weight = 14294.749|
|-----------------------------------------------------------------------------|
r_work (final): 0.3704
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7728
moved from start:          0.3251

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.042  10545  Z= 0.092
  Angle     :  0.438   5.557  14364  Z= 0.242
  Chirality :  0.035   0.160   1613
  Planarity :  0.003   0.043   1702
  Dihedral  : 18.281 175.233   1866
  Min Nonbonded Distance : 2.380

Molprobity Statistics.
  All-atom Clashscore : 1.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.60 %
    Favored  : 95.40 %
  Rotamer:
    Outliers :  1.06 %
    Allowed  :  9.44 %
    Favored  : 89.50 %
  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 are not related in a simple way.
  whole:  1.86 (0.26), residues: 1152
  helix:  2.91 (0.23), residues: 549
  sheet:  0.80 (0.49), residues: 117
  loop : -0.69 (0.29), residues: 486

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 768 
 TYR   0.008   0.001   TYR A 763 
 PHE   0.018   0.001   PHE A 939 
 TRP   0.010   0.001   TRP A 466 
 HIS   0.002   0.000   HIS A 955 

Details of bonding type rmsd
  covalent geometry    : bond        0.00200 (10545)
  covalent geometry    : angle       0.43789 (14364)
  hydrogen bonds       : bond        0.03221 (  485)
  hydrogen bonds       : angle       3.85120 ( 1380)

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

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

  2304 Ramachandran restraints generated.
    1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2304 Ramachandran restraints generated.
    1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 100
  time to evaluate  : 0.426 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  797 MET cc_start: 0.8505 (tmm) cc_final: 0.8075 (tmm)
REVERT: A  845 GLU cc_start: 0.7959 (tp30) cc_final: 0.7746 (tp30)
REVERT: A  987 ASP cc_start: 0.6506 (t0) cc_final: 0.6296 (t0)
REVERT: A 1124 LYS cc_start: 0.8556 (mmmt) cc_final: 0.8136 (mtpp)
  outliers start: 11
  outliers final: 9
  residues processed: 108
  average time/residue: 0.2155
  time to fit residues: 33.6271
Evaluate side-chains
  100 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 91
  time to evaluate  : 0.465 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   95 LEU
Chi-restraints excluded: chain A residue  198 VAL
Chi-restraints excluded: chain A residue  380 MET
Chi-restraints excluded: chain A residue  454 LEU
Chi-restraints excluded: chain A residue  606 ILE
Chi-restraints excluded: chain A residue  808 LEU
Chi-restraints excluded: chain A residue  934 LEU
Chi-restraints excluded: chain A residue 1073 SER
Chi-restraints excluded: chain A residue 1089 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 33 optimal weight:   10.0000
   chunk 113 optimal weight:    4.9990
   chunk 38 optimal weight:    1.9990
   chunk 41 optimal weight:    6.9990
   chunk 42 optimal weight:    2.9990
   chunk 26 optimal weight:    9.9990
   chunk 104 optimal weight:    1.9990
   chunk 67 optimal weight:    2.9990
   chunk 10 optimal weight:    4.9990
   chunk 82 optimal weight:    2.9990
   chunk 45 optimal weight:    2.9990
   overall best weight:    2.5990

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4167 r_free = 0.4167 target = 0.184698 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3650 r_free = 0.3650 target = 0.137414 restraints weight = 40558.845|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3659 r_free = 0.3659 target = 0.140252 restraints weight = 28170.385|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3680 r_free = 0.3680 target = 0.142511 restraints weight = 22802.905|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3688 r_free = 0.3688 target = 0.143322 restraints weight = 15880.815|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3693 r_free = 0.3693 target = 0.143868 restraints weight = 15539.357|
|-----------------------------------------------------------------------------|
r_work (final): 0.3704
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7765
moved from start:          0.3364

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.038  10545  Z= 0.214
  Angle     :  0.511   5.241  14364  Z= 0.285
  Chirality :  0.037   0.179   1613
  Planarity :  0.003   0.047   1702
  Dihedral  : 18.449 176.675   1866
  Min Nonbonded Distance : 2.323

Molprobity Statistics.
  All-atom Clashscore : 2.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.47 %
    Favored  : 94.53 %
  Rotamer:
    Outliers :  1.45 %
    Allowed  :  9.63 %
    Favored  : 88.92 %
  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 are not related in a simple way.
  whole:  1.57 (0.26), residues: 1152
  helix:  2.67 (0.23), residues: 549
  sheet:  0.61 (0.49), residues: 117
  loop : -0.83 (0.28), residues: 486

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 768 
 TYR   0.012   0.002   TYR A 659 
 PHE   0.020   0.001   PHE A 939 
 TRP   0.011   0.001   TRP A 466 
 HIS   0.005   0.001   HIS A 838 

Details of bonding type rmsd
  covalent geometry    : bond        0.00498 (10545)
  covalent geometry    : angle       0.51051 (14364)
  hydrogen bonds       : bond        0.04282 (  485)
  hydrogen bonds       : angle       4.09057 ( 1380)

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

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

  2304 Ramachandran restraints generated.
    1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2304 Ramachandran restraints generated.
    1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 99
  time to evaluate  : 0.397 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  797 MET cc_start: 0.8594 (tmm) cc_final: 0.8131 (tmm)
REVERT: A  845 GLU cc_start: 0.8142 (tp30) cc_final: 0.7923 (tp30)
REVERT: A 1124 LYS cc_start: 0.8580 (mmmt) cc_final: 0.8160 (mtpp)
  outliers start: 15
  outliers final: 12
  residues processed: 110
  average time/residue: 0.2037
  time to fit residues: 32.3985
Evaluate side-chains
  107 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 95
  time to evaluate  : 0.480 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 LEU
Chi-restraints excluded: chain A residue   95 LEU
Chi-restraints excluded: chain A residue  170 SER
Chi-restraints excluded: chain A residue  198 VAL
Chi-restraints excluded: chain A residue  454 LEU
Chi-restraints excluded: chain A residue  606 ILE
Chi-restraints excluded: chain A residue  680 ILE
Chi-restraints excluded: chain A residue  715 GLU
Chi-restraints excluded: chain A residue  808 LEU
Chi-restraints excluded: chain A residue  934 LEU
Chi-restraints excluded: chain A residue 1073 SER
Chi-restraints excluded: chain A residue 1089 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 90 optimal weight:    9.9990
   chunk 86 optimal weight:    3.9990
   chunk 114 optimal weight:    0.9980
   chunk 19 optimal weight:    1.9990
   chunk 15 optimal weight:    1.9990
   chunk 37 optimal weight:    9.9990
   chunk 0 optimal weight:    1.9990
   chunk 88 optimal weight:    6.9990
   chunk 99 optimal weight:    1.9990
   chunk 73 optimal weight:    1.9990
   chunk 6 optimal weight:    0.9980
   overall best weight:    1.5986

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

Flipped N/Q/H residues before XYZ refinement:
A 986 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4176 r_free = 0.4176 target = 0.185455 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3660 r_free = 0.3660 target = 0.138353 restraints weight = 40490.474|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3668 r_free = 0.3668 target = 0.141145 restraints weight = 28282.263|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.143429 restraints weight = 22331.417|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3704 r_free = 0.3704 target = 0.145007 restraints weight = 16448.826|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3715 r_free = 0.3715 target = 0.146433 restraints weight = 15391.214|
|-----------------------------------------------------------------------------|
r_work (final): 0.3726
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7718
moved from start:          0.3528

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028  10545  Z= 0.136
  Angle     :  0.463   4.875  14364  Z= 0.258
  Chirality :  0.036   0.167   1613
  Planarity :  0.003   0.046   1702
  Dihedral  : 18.423 177.196   1866
  Min Nonbonded Distance : 2.362

Molprobity Statistics.
  All-atom Clashscore : 2.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.95 %
    Favored  : 95.05 %
  Rotamer:
    Outliers :  1.35 %
    Allowed  : 10.21 %
    Favored  : 88.44 %
  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 are not related in a simple way.
  whole:  1.52 (0.26), residues: 1152
  helix:  2.71 (0.23), residues: 546
  sheet:  0.45 (0.48), residues: 117
  loop : -0.89 (0.28), residues: 489

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A1147 
 TYR   0.014   0.001   TYR A 326 
 PHE   0.025   0.001   PHE A 254 
 TRP   0.012   0.001   TRP A 466 
 HIS   0.003   0.001   HIS A 673 

Details of bonding type rmsd
  covalent geometry    : bond        0.00311 (10545)
  covalent geometry    : angle       0.46297 (14364)
  hydrogen bonds       : bond        0.03878 (  485)
  hydrogen bonds       : angle       3.96275 ( 1380)

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

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

  2304 Ramachandran restraints generated.
    1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2304 Ramachandran restraints generated.
    1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 95
  time to evaluate  : 0.532 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  797 MET cc_start: 0.8579 (tmm) cc_final: 0.8141 (tmm)
REVERT: A  845 GLU cc_start: 0.8099 (tp30) cc_final: 0.7856 (tp30)
REVERT: A 1124 LYS cc_start: 0.8582 (mmmt) cc_final: 0.8142 (mtpp)
  outliers start: 14
  outliers final: 13
  residues processed: 105
  average time/residue: 0.2157
  time to fit residues: 32.8501
Evaluate side-chains
  104 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 91
  time to evaluate  : 0.552 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   49 VAL
Chi-restraints excluded: chain A residue   86 LEU
Chi-restraints excluded: chain A residue   95 LEU
Chi-restraints excluded: chain A residue   98 HIS
Chi-restraints excluded: chain A residue  198 VAL
Chi-restraints excluded: chain A residue  380 MET
Chi-restraints excluded: chain A residue  454 LEU
Chi-restraints excluded: chain A residue  606 ILE
Chi-restraints excluded: chain A residue  715 GLU
Chi-restraints excluded: chain A residue  808 LEU
Chi-restraints excluded: chain A residue  934 LEU
Chi-restraints excluded: chain A residue 1073 SER
Chi-restraints excluded: chain A residue 1089 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 111 optimal weight:    6.9990
   chunk 11 optimal weight:    2.9990
   chunk 47 optimal weight:    2.9990
   chunk 6 optimal weight:    0.0980
   chunk 24 optimal weight:    5.9990
   chunk 118 optimal weight:   10.0000
   chunk 103 optimal weight:    4.9990
   chunk 44 optimal weight:    2.9990
   chunk 46 optimal weight:    2.9990
   chunk 107 optimal weight:    0.6980
   chunk 91 optimal weight:    8.9990
   overall best weight:    1.9586

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

Flipped N/Q/H residues before XYZ refinement:
A 986 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4163 r_free = 0.4163 target = 0.184120 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3649 r_free = 0.3649 target = 0.137284 restraints weight = 40625.522|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3637 r_free = 0.3637 target = 0.138491 restraints weight = 29532.660|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3664 r_free = 0.3664 target = 0.141475 restraints weight = 25159.275|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3669 r_free = 0.3669 target = 0.141948 restraints weight = 16279.402|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3676 r_free = 0.3676 target = 0.142706 restraints weight = 15775.513|
|-----------------------------------------------------------------------------|
r_work (final): 0.3702
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7778
moved from start:          0.3658

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039  10545  Z= 0.168
  Angle     :  0.489   5.404  14364  Z= 0.273
  Chirality :  0.036   0.173   1613
  Planarity :  0.003   0.047   1702
  Dihedral  : 18.469 178.072   1866
  Min Nonbonded Distance : 2.302

Molprobity Statistics.
  All-atom Clashscore : 2.57
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  6.08 %
    Favored  : 93.84 %
  Rotamer:
    Outliers :  1.54 %
    Allowed  : 10.79 %
    Favored  : 87.67 %
  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 are not related in a simple way.
  whole:  1.37 (0.26), residues: 1152
  helix:  2.61 (0.23), residues: 546
  sheet:  0.35 (0.49), residues: 117
  loop : -1.00 (0.27), residues: 489

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 768 
 TYR   0.013   0.001   TYR A 326 
 PHE   0.021   0.001   PHE A 254 
 TRP   0.011   0.001   TRP A 466 
 HIS   0.003   0.001   HIS A 838 

Details of bonding type rmsd
  covalent geometry    : bond        0.00387 (10545)
  covalent geometry    : angle       0.48931 (14364)
  hydrogen bonds       : bond        0.04104 (  485)
  hydrogen bonds       : angle       4.00058 ( 1380)

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

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

  2304 Ramachandran restraints generated.
    1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2304 Ramachandran restraints generated.
    1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 92
  time to evaluate  : 0.549 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  403 LYS cc_start: 0.8937 (tptm) cc_final: 0.8286 (tppp)
REVERT: A  797 MET cc_start: 0.8597 (tmm) cc_final: 0.8160 (tmm)
REVERT: A  845 GLU cc_start: 0.8126 (tp30) cc_final: 0.7901 (tp30)
REVERT: A  897 TRP cc_start: 0.7441 (t-100) cc_final: 0.7188 (t-100)
  outliers start: 16
  outliers final: 15
  residues processed: 105
  average time/residue: 0.2122
  time to fit residues: 32.1696
Evaluate side-chains
  106 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 91
  time to evaluate  : 0.546 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   49 VAL
Chi-restraints excluded: chain A residue   86 LEU
Chi-restraints excluded: chain A residue   95 LEU
Chi-restraints excluded: chain A residue   98 HIS
Chi-restraints excluded: chain A residue  170 SER
Chi-restraints excluded: chain A residue  198 VAL
Chi-restraints excluded: chain A residue  454 LEU
Chi-restraints excluded: chain A residue  487 ASN
Chi-restraints excluded: chain A residue  606 ILE
Chi-restraints excluded: chain A residue  680 ILE
Chi-restraints excluded: chain A residue  715 GLU
Chi-restraints excluded: chain A residue  808 LEU
Chi-restraints excluded: chain A residue  934 LEU
Chi-restraints excluded: chain A residue 1073 SER
Chi-restraints excluded: chain A residue 1089 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 27 optimal weight:    7.9990
   chunk 112 optimal weight:    0.8980
   chunk 69 optimal weight:    3.9990
   chunk 33 optimal weight:    9.9990
   chunk 102 optimal weight:    1.9990
   chunk 10 optimal weight:    3.9990
   chunk 35 optimal weight:   20.0000
   chunk 85 optimal weight:    0.0980
   chunk 31 optimal weight:    0.9990
   chunk 2 optimal weight:    0.0770
   chunk 78 optimal weight:    0.8980
   overall best weight:    0.5940

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

Flipped N/Q/H residues before XYZ refinement:
A 986 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4199 r_free = 0.4199 target = 0.187736 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3693 r_free = 0.3693 target = 0.140795 restraints weight = 40422.823|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3717 r_free = 0.3717 target = 0.144837 restraints weight = 27498.611|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3725 r_free = 0.3725 target = 0.146251 restraints weight = 22669.794|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3737 r_free = 0.3737 target = 0.147323 restraints weight = 15462.633|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3740 r_free = 0.3740 target = 0.147827 restraints weight = 14572.354|
|-----------------------------------------------------------------------------|
r_work (final): 0.3746
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7694
moved from start:          0.3772

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.041  10545  Z= 0.089
  Angle     :  0.440   4.873  14364  Z= 0.241
  Chirality :  0.035   0.165   1613
  Planarity :  0.003   0.044   1702
  Dihedral  : 18.258 177.236   1866
  Min Nonbonded Distance : 2.366

Molprobity Statistics.
  All-atom Clashscore : 2.17
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.60 %
    Favored  : 95.31 %
  Rotamer:
    Outliers :  1.35 %
    Allowed  : 10.98 %
    Favored  : 87.67 %
  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 are not related in a simple way.
  whole:  1.64 (0.26), residues: 1152
  helix:  2.79 (0.23), residues: 550
  sheet:  0.47 (0.49), residues: 117
  loop : -0.82 (0.28), residues: 485

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 768 
 TYR   0.010   0.001   TYR A 326 
 PHE   0.020   0.001   PHE A 939 
 TRP   0.013   0.001   TRP A 466 
 HIS   0.002   0.001   HIS A 838 

Details of bonding type rmsd
  covalent geometry    : bond        0.00192 (10545)
  covalent geometry    : angle       0.44000 (14364)
  hydrogen bonds       : bond        0.03225 (  485)
  hydrogen bonds       : angle       3.74883 ( 1380)

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

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

  2304 Ramachandran restraints generated.
    1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2304 Ramachandran restraints generated.
    1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 96
  time to evaluate  : 0.572 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   87 GLU cc_start: 0.8368 (mm-30) cc_final: 0.7556 (tm-30)
REVERT: A  403 LYS cc_start: 0.8889 (tptm) cc_final: 0.8248 (tppp)
REVERT: A  797 MET cc_start: 0.8552 (tmm) cc_final: 0.8105 (tmm)
REVERT: A  845 GLU cc_start: 0.8064 (tp30) cc_final: 0.7820 (tp30)
REVERT: A  897 TRP cc_start: 0.7405 (t-100) cc_final: 0.7156 (t-100)
  outliers start: 14
  outliers final: 13
  residues processed: 108
  average time/residue: 0.2211
  time to fit residues: 34.2498
Evaluate side-chains
  105 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 92
  time to evaluate  : 0.478 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   49 VAL
Chi-restraints excluded: chain A residue   86 LEU
Chi-restraints excluded: chain A residue   95 LEU
Chi-restraints excluded: chain A residue   98 HIS
Chi-restraints excluded: chain A residue  170 SER
Chi-restraints excluded: chain A residue  198 VAL
Chi-restraints excluded: chain A residue  454 LEU
Chi-restraints excluded: chain A residue  606 ILE
Chi-restraints excluded: chain A residue  715 GLU
Chi-restraints excluded: chain A residue  808 LEU
Chi-restraints excluded: chain A residue  934 LEU
Chi-restraints excluded: chain A residue 1073 SER
Chi-restraints excluded: chain A residue 1089 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 20 optimal weight:    3.9990
   chunk 41 optimal weight:    6.9990
   chunk 51 optimal weight:    2.9990
   chunk 103 optimal weight:    4.9990
   chunk 10 optimal weight:    0.4980
   chunk 112 optimal weight:    4.9990
   chunk 9 optimal weight:    2.9990
   chunk 38 optimal weight:    6.9990
   chunk 19 optimal weight:    1.9990
   chunk 14 optimal weight:    1.9990
   chunk 50 optimal weight:    2.9990
   overall best weight:    2.0988

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

Flipped N/Q/H residues before XYZ refinement:
A 434 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4153 r_free = 0.4153 target = 0.183087 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3633 r_free = 0.3633 target = 0.136011 restraints weight = 40860.168|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3642 r_free = 0.3642 target = 0.138757 restraints weight = 28732.706|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3662 r_free = 0.3662 target = 0.141047 restraints weight = 22506.555|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3680 r_free = 0.3680 target = 0.142746 restraints weight = 16527.759|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3690 r_free = 0.3690 target = 0.144049 restraints weight = 15660.559|
|-----------------------------------------------------------------------------|
r_work (final): 0.3712
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7749
moved from start:          0.3885

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034  10545  Z= 0.180
  Angle     :  0.499   5.365  14364  Z= 0.278
  Chirality :  0.037   0.175   1613
  Planarity :  0.003   0.048   1702
  Dihedral  : 18.457 178.655   1866
  Min Nonbonded Distance : 2.338

Molprobity Statistics.
  All-atom Clashscore : 3.31
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  6.08 %
    Favored  : 93.84 %
  Rotamer:
    Outliers :  1.35 %
    Allowed  : 10.98 %
    Favored  : 87.67 %
  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 are not related in a simple way.
  whole:  1.36 (0.26), residues: 1152
  helix:  2.61 (0.23), residues: 546
  sheet:  0.31 (0.49), residues: 117
  loop : -0.99 (0.28), residues: 489

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 639 
 TYR   0.012   0.001   TYR A 326 
 PHE   0.018   0.001   PHE A 254 
 TRP   0.009   0.001   TRP A 466 
 HIS   0.004   0.001   HIS A 838 

Details of bonding type rmsd
  covalent geometry    : bond        0.00420 (10545)
  covalent geometry    : angle       0.49870 (14364)
  hydrogen bonds       : bond        0.04310 (  485)
  hydrogen bonds       : angle       3.97900 ( 1380)

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

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

  2304 Ramachandran restraints generated.
    1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2304 Ramachandran restraints generated.
    1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 89
  time to evaluate  : 0.394 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  403 LYS cc_start: 0.8929 (tptm) cc_final: 0.8276 (tppp)
REVERT: A  797 MET cc_start: 0.8566 (tmm) cc_final: 0.8122 (tmm)
REVERT: A  845 GLU cc_start: 0.8161 (tp30) cc_final: 0.7931 (tp30)
REVERT: A  897 TRP cc_start: 0.7421 (t-100) cc_final: 0.7161 (t-100)
  outliers start: 14
  outliers final: 14
  residues processed: 101
  average time/residue: 0.2207
  time to fit residues: 31.4836
Evaluate side-chains
  103 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 89
  time to evaluate  : 0.497 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    4 TYR
Chi-restraints excluded: chain A residue   49 VAL
Chi-restraints excluded: chain A residue   86 LEU
Chi-restraints excluded: chain A residue   95 LEU
Chi-restraints excluded: chain A residue   98 HIS
Chi-restraints excluded: chain A residue  170 SER
Chi-restraints excluded: chain A residue  198 VAL
Chi-restraints excluded: chain A residue  454 LEU
Chi-restraints excluded: chain A residue  606 ILE
Chi-restraints excluded: chain A residue  715 GLU
Chi-restraints excluded: chain A residue  808 LEU
Chi-restraints excluded: chain A residue  934 LEU
Chi-restraints excluded: chain A residue 1073 SER
Chi-restraints excluded: chain A residue 1089 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 33 optimal weight:   10.0000
   chunk 22 optimal weight:    3.9990
   chunk 63 optimal weight:    0.9990
   chunk 85 optimal weight:    0.9980
   chunk 32 optimal weight:    8.9990
   chunk 60 optimal weight:    1.9990
   chunk 14 optimal weight:    2.9990
   chunk 2 optimal weight:    1.9990
   chunk 5 optimal weight:    3.9990
   chunk 42 optimal weight:    1.9990
   chunk 13 optimal weight:    0.5980
   overall best weight:    1.3186

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4173 r_free = 0.4173 target = 0.184967 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3657 r_free = 0.3657 target = 0.137873 restraints weight = 40674.540|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3672 r_free = 0.3672 target = 0.141288 restraints weight = 28624.158|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3688 r_free = 0.3688 target = 0.143231 restraints weight = 22298.909|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3700 r_free = 0.3700 target = 0.144369 restraints weight = 16023.262|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3703 r_free = 0.3703 target = 0.144705 restraints weight = 15348.894|
|-----------------------------------------------------------------------------|
r_work (final): 0.3712
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7744
moved from start:          0.3957

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  10545  Z= 0.123
  Angle     :  0.460   4.758  14364  Z= 0.255
  Chirality :  0.035   0.167   1613
  Planarity :  0.003   0.045   1702
  Dihedral  : 18.380 178.595   1866
  Min Nonbonded Distance : 2.370

Molprobity Statistics.
  All-atom Clashscore : 2.72
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  5.47 %
    Favored  : 94.44 %
  Rotamer:
    Outliers :  1.35 %
    Allowed  : 10.98 %
    Favored  : 87.67 %
  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 are not related in a simple way.
  whole:  1.44 (0.26), residues: 1152
  helix:  2.67 (0.23), residues: 547
  sheet:  0.30 (0.49), residues: 117
  loop : -0.94 (0.28), residues: 488

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 768 
 TYR   0.009   0.001   TYR A 326 
 PHE   0.018   0.001   PHE A 254 
 TRP   0.012   0.001   TRP A 466 
 HIS   0.003   0.001   HIS A 838 

Details of bonding type rmsd
  covalent geometry    : bond        0.00280 (10545)
  covalent geometry    : angle       0.46010 (14364)
  hydrogen bonds       : bond        0.03794 (  485)
  hydrogen bonds       : angle       3.87188 ( 1380)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2712.83 seconds
wall clock time: 47 minutes 9.29 seconds (2829.29 seconds total)