Starting phenix.real_space_refine
on Fri May 16 21:57:07 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8u7o_41987/05_2025/8u7o_41987.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8u7o_41987/05_2025/8u7o_41987.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8u7o_41987/05_2025/8u7o_41987.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8u7o_41987/05_2025/8u7o_41987.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8u7o_41987/05_2025/8u7o_41987.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8u7o_41987/05_2025/8u7o_41987.cif"
  }
  resolution = 3.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.017 sd=   0.106
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: 5
    Type Number    sf(0)   Gaussians
     P       5      5.49       5
     S      65      5.16       5
     C    9703      2.51       5
     N    2434      2.21       5
     O    2722      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 3 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 14929
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 7227
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 978, 7227
          Classifications: {'peptide': 978}
          Incomplete info: {'truncation_to_alanine': 135}
          Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 949}
          Chain breaks: 5
          Unresolved non-hydrogen bonds: 518
          Unresolved non-hydrogen angles: 654
          Unresolved non-hydrogen dihedrals: 417
          Unresolved non-hydrogen chiralities: 58
          Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 4, 'TYR:plan': 3, 'ASN:plan1': 4, 'ASP:plan': 6, 'PHE:plan': 9, 'GLU:plan': 16, 'ARG:plan': 13}
          Unresolved non-hydrogen planarities: 269
    Chain: "B"
      Number of atoms: 7248
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 981, 7248
          Classifications: {'peptide': 981}
          Incomplete info: {'truncation_to_alanine': 136}
          Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 952}
          Chain breaks: 5
          Unresolved non-hydrogen bonds: 521
          Unresolved non-hydrogen angles: 657
          Unresolved non-hydrogen dihedrals: 420
          Unresolved non-hydrogen chiralities: 57
          Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 4, 'TYR:plan': 3, 'ASN:plan1': 5, 'ASP:plan': 6, 'PHE:plan': 9, 'GLU:plan': 17, 'ARG:plan': 13}
          Unresolved non-hydrogen planarities: 272
    Chain: "A"
      Number of atoms: 134
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 134
          Unusual residues: {'AJP': 1, 'POV': 1}
          Classifications: {'RNA': 1, 'undetermined': 2}
          Modifications used: {'rna3p': 1}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 26
          Unresolved non-hydrogen angles: 38
          Unresolved non-hydrogen dihedrals: 36
          Unresolved non-hydrogen chiralities: 5
    Chain: "B"
      Number of atoms: 320
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 6, 320
          Unusual residues: {'AJP': 3, 'POV': 2}
          Classifications: {'RNA': 1, 'undetermined': 5}
          Modifications used: {'rna3p': 1}
          Link IDs: {None: 5}
          Unresolved non-hydrogen bonds: 64
          Unresolved non-hydrogen angles: 93
          Unresolved non-hydrogen dihedrals: 99
          Unresolved non-hydrogen chiralities: 15
  Time building chain proxies: 9.06, per 1000 atoms: 0.61
  Number of scatterers: 14929
  At special positions: 0
  Unit cell: (111.78, 142.14, 133.86, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      65     16.00
     P       5     15.00
     O    2722      8.00
     N    2434      7.00
     C    9703      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 4.54
  Conformation dependent library (CDL) restraints added in 2.4 seconds
  

  3870 Ramachandran restraints generated.
    1935 Oldfield, 0 Emsley, 1935 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3690

  Finding SS restraints...
    Secondary structure from input PDB file:
      81 helices and 8 sheets defined
      73.8% alpha, 5.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 2.05
  Creating SS restraints...
    Processing helix  chain 'A' and resid 77 through 95
    Processing helix  chain 'A' and resid 102 through 118
      removed outlier: 3.677A  pdb=" N   LEU A 106 " --> pdb=" O   TYR A 102 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 120 through 131
    Processing helix  chain 'A' and resid 134 through 151
      removed outlier: 3.939A  pdb=" N   LEU A 138 " --> pdb=" O   ASP A 134 " (cutoff:3.500A)
      removed outlier: 5.101A  pdb=" N   LEU A 143 " --> pdb=" O   LEU A 139 " (cutoff:3.500A)
      Proline residue:  A 144  - end of helix
    Processing helix  chain 'A' and resid 155 through 161
    Processing helix  chain 'A' and resid 162 through 189
    Processing helix  chain 'A' and resid 194 through 207
      removed outlier: 3.817A  pdb=" N   ALA A 207 " --> pdb=" O   ALA A 203 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 210 through 221
    Processing helix  chain 'A' and resid 224 through 253
      removed outlier: 3.700A  pdb=" N   THR A 228 " --> pdb=" O   LYS A 224 " (cutoff:3.500A)
      removed outlier: 4.238A  pdb=" N   MET A 251 " --> pdb=" O   VAL A 247 " (cutoff:3.500A)
      removed outlier: 3.524A  pdb=" N   PHE A 253 " --> pdb=" O   MET A 249 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 260 through 291
      removed outlier: 3.904A  pdb=" N   LEU A 266 " --> pdb=" O   GLY A 262 " (cutoff:3.500A)
      removed outlier: 4.545A  pdb=" N   GLY A 275 " --> pdb=" O   VAL A 271 " (cutoff:3.500A)
      Proline residue:  A 276  - end of helix
    Processing helix  chain 'A' and resid 297 through 319
      removed outlier: 3.507A  pdb=" N   ILE A 301 " --> pdb=" O   ALA A 297 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 321 through 337
      removed outlier: 4.070A  pdb=" N   LEU A 325 " --> pdb=" O   VAL A 321 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 342 through 376
    Processing helix  chain 'A' and resid 377 through 379
      No H-bonds generated for 'chain 'A' and resid 377 through 379'
    Processing helix  chain 'A' and resid 381 through 414
      removed outlier: 3.955A  pdb=" N   TRP A 385 " --> pdb=" O   ASP A 381 " (cutoff:3.500A)
      removed outlier: 4.599A  pdb=" N   ILE A 389 " --> pdb=" O   TRP A 385 " (cutoff:3.500A)
      removed outlier: 3.786A  pdb=" N   ILE A 390 " --> pdb=" O   PHE A 386 " (cutoff:3.500A)
      removed outlier: 3.977A  pdb=" N   ILE A 403 " --> pdb=" O   ARG A 399 " (cutoff:3.500A)
      Proline residue:  A 408  - end of helix
    Processing helix  chain 'A' and resid 418 through 427
      removed outlier: 4.188A  pdb=" N   TRP A 427 " --> pdb=" O   VAL A 423 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 433 through 446
    Processing helix  chain 'A' and resid 449 through 482
      removed outlier: 4.217A  pdb=" N   SER A 453 " --> pdb=" O   ASP A 449 " (cutoff:3.500A)
      removed outlier: 4.316A  pdb=" N   VAL A 468 " --> pdb=" O   VAL A 464 " (cutoff:3.500A)
      removed outlier: 4.357A  pdb=" N   ALA A 471 " --> pdb=" O   LEU A 467 " (cutoff:3.500A)
      removed outlier: 3.770A  pdb=" N   GLY A 482 " --> pdb=" O   LEU A 478 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 487 through 514
      removed outlier: 3.839A  pdb=" N   SER A 514 " --> pdb=" O   ASN A 510 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 522 through 530
      removed outlier: 3.528A  pdb=" N   ALA A 526 " --> pdb=" O   ASP A 522 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 573 through 601
    Processing helix  chain 'A' and resid 605 through 618
      removed outlier: 3.680A  pdb=" N   ALA A 618 " --> pdb=" O   HIS A 614 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 628 through 636
    Processing helix  chain 'A' and resid 639 through 652
      removed outlier: 4.322A  pdb=" N   TRP A 643 " --> pdb=" O   GLY A 639 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   ASP A 650 " --> pdb=" O   ARG A 646 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 678 through 692
    Processing helix  chain 'A' and resid 694 through 700
    Processing helix  chain 'A' and resid 730 through 753
    Processing helix  chain 'A' and resid 761 through 774
      removed outlier: 3.886A  pdb=" N   PHE A 766 " --> pdb=" O   HIS A 762 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 809 through 858
      Proline residue:  A 819  - end of helix
      removed outlier: 3.565A  pdb=" N   GLN A 832 " --> pdb=" O   LYS A 828 " (cutoff:3.500A)
      removed outlier: 3.927A  pdb=" N   LYS A 852 " --> pdb=" O   GLU A 848 " (cutoff:3.500A)
      removed outlier: 4.067A  pdb=" N   ILE A 853 " --> pdb=" O   GLU A 849 " (cutoff:3.500A)
      removed outlier: 4.486A  pdb=" N   ASP A 855 " --> pdb=" O   GLY A 851 " (cutoff:3.500A)
      removed outlier: 4.902A  pdb=" N   ARG A 856 " --> pdb=" O   LYS A 852 " (cutoff:3.500A)
      removed outlier: 3.575A  pdb=" N   MET A 857 " --> pdb=" O   ILE A 853 " (cutoff:3.500A)
      removed outlier: 3.730A  pdb=" N   VAL A 858 " --> pdb=" O   ILE A 854 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 860 through 889
      removed outlier: 3.882A  pdb=" N   LYS A 880 " --> pdb=" O   LEU A 876 " (cutoff:3.500A)
      removed outlier: 3.838A  pdb=" N   GLU A 881 " --> pdb=" O   GLN A 877 " (cutoff:3.500A)
      removed outlier: 3.775A  pdb=" N   HIS A 889 " --> pdb=" O   LEU A 885 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 890 through 919
      removed outlier: 3.536A  pdb=" N   VAL A 894 " --> pdb=" O   PRO A 890 " (cutoff:3.500A)
      removed outlier: 4.296A  pdb=" N   ILE A 902 " --> pdb=" O   THR A 898 " (cutoff:3.500A)
      removed outlier: 4.203A  pdb=" N   ARG A 903 " --> pdb=" O   ARG A 899 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 923 through 943
      removed outlier: 3.915A  pdb=" N   THR A 933 " --> pdb=" O   LYS A 929 " (cutoff:3.500A)
      removed outlier: 3.617A  pdb=" N   VAL A 934 " --> pdb=" O   LEU A 930 " (cutoff:3.500A)
      removed outlier: 3.824A  pdb=" N   ASN A 943 " --> pdb=" O   LYS A 939 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 954 through 962
      removed outlier: 3.995A  pdb=" N   TRP A 962 " --> pdb=" O   LYS A 958 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 966 through 975
    Processing helix  chain 'A' and resid 1044 through 1049
      removed outlier: 3.603A  pdb=" N   LEU A1048 " --> pdb=" O   GLU A1044 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1070 through 1080
      removed outlier: 3.577A  pdb=" N   PHE A1080 " --> pdb=" O   ALA A1076 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1084 through 1100
    Processing helix  chain 'A' and resid 1100 through 1105
      removed outlier: 3.920A  pdb=" N   MET A1104 " --> pdb=" O   THR A1100 " (cutoff:3.500A)
      removed outlier: 4.164A  pdb=" N   GLU A1105 " --> pdb=" O   PRO A1101 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 1100 through 1105'
    Processing helix  chain 'A' and resid 1113 through 1121
    Processing helix  chain 'B' and resid 77 through 95
    Processing helix  chain 'B' and resid 102 through 118
      removed outlier: 3.666A  pdb=" N   LEU B 106 " --> pdb=" O   TYR B 102 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 120 through 132
      removed outlier: 3.984A  pdb=" N   HIS B 132 " --> pdb=" O   ARG B 128 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 134 through 151
      removed outlier: 3.827A  pdb=" N   LEU B 138 " --> pdb=" O   ASP B 134 " (cutoff:3.500A)
      removed outlier: 5.089A  pdb=" N   LEU B 143 " --> pdb=" O   LEU B 139 " (cutoff:3.500A)
      Proline residue:  B 144  - end of helix
    Processing helix  chain 'B' and resid 155 through 161
    Processing helix  chain 'B' and resid 162 through 189
    Processing helix  chain 'B' and resid 194 through 207
      removed outlier: 3.724A  pdb=" N   ALA B 207 " --> pdb=" O   ALA B 203 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 210 through 221
    Processing helix  chain 'B' and resid 224 through 254
      removed outlier: 3.714A  pdb=" N   THR B 228 " --> pdb=" O   LYS B 224 " (cutoff:3.500A)
      removed outlier: 3.737A  pdb=" N   PHE B 254 " --> pdb=" O   LYS B 250 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 260 through 291
      removed outlier: 3.919A  pdb=" N   LEU B 266 " --> pdb=" O   GLY B 262 " (cutoff:3.500A)
      removed outlier: 4.627A  pdb=" N   GLY B 275 " --> pdb=" O   VAL B 271 " (cutoff:3.500A)
      Proline residue:  B 276  - end of helix
    Processing helix  chain 'B' and resid 297 through 319
      removed outlier: 3.520A  pdb=" N   ILE B 301 " --> pdb=" O   ALA B 297 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 321 through 337
      removed outlier: 4.010A  pdb=" N   LEU B 325 " --> pdb=" O   VAL B 321 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 342 through 376
    Processing helix  chain 'B' and resid 377 through 379
      No H-bonds generated for 'chain 'B' and resid 377 through 379'
    Processing helix  chain 'B' and resid 381 through 414
      removed outlier: 3.983A  pdb=" N   TRP B 385 " --> pdb=" O   ASP B 381 " (cutoff:3.500A)
      removed outlier: 4.234A  pdb=" N   ILE B 389 " --> pdb=" O   TRP B 385 " (cutoff:3.500A)
      removed outlier: 3.752A  pdb=" N   ILE B 390 " --> pdb=" O   PHE B 386 " (cutoff:3.500A)
      removed outlier: 3.977A  pdb=" N   ILE B 403 " --> pdb=" O   ARG B 399 " (cutoff:3.500A)
      Proline residue:  B 408  - end of helix
    Processing helix  chain 'B' and resid 418 through 427
      removed outlier: 4.067A  pdb=" N   TRP B 427 " --> pdb=" O   VAL B 423 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 433 through 445
    Processing helix  chain 'B' and resid 449 through 482
      removed outlier: 4.224A  pdb=" N   SER B 453 " --> pdb=" O   ASP B 449 " (cutoff:3.500A)
      removed outlier: 4.333A  pdb=" N   VAL B 468 " --> pdb=" O   VAL B 464 " (cutoff:3.500A)
      removed outlier: 4.359A  pdb=" N   ALA B 471 " --> pdb=" O   LEU B 467 " (cutoff:3.500A)
      removed outlier: 3.736A  pdb=" N   GLY B 482 " --> pdb=" O   LEU B 478 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 487 through 514
      removed outlier: 3.793A  pdb=" N   SER B 514 " --> pdb=" O   ASN B 510 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 522 through 530
      removed outlier: 3.529A  pdb=" N   ALA B 526 " --> pdb=" O   ASP B 522 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 573 through 601
    Processing helix  chain 'B' and resid 605 through 618
      removed outlier: 3.602A  pdb=" N   ALA B 618 " --> pdb=" O   HIS B 614 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 628 through 636
    Processing helix  chain 'B' and resid 639 through 652
      removed outlier: 4.363A  pdb=" N   TRP B 643 " --> pdb=" O   GLY B 639 " (cutoff:3.500A)
      removed outlier: 3.629A  pdb=" N   ASP B 650 " --> pdb=" O   ARG B 646 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 679 through 691
    Processing helix  chain 'B' and resid 691 through 700
      removed outlier: 3.596A  pdb=" N   ILE B 695 " --> pdb=" O   ASN B 691 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 730 through 753
    Processing helix  chain 'B' and resid 754 through 756
      No H-bonds generated for 'chain 'B' and resid 754 through 756'
    Processing helix  chain 'B' and resid 763 through 774
      removed outlier: 4.139A  pdb=" N   ASP B 767 " --> pdb=" O   TRP B 763 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 808 through 812
      removed outlier: 4.516A  pdb=" N   LEU B 811 " --> pdb=" O   LEU B 808 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 813 through 852
      Proline residue:  B 819  - end of helix
      removed outlier: 3.763A  pdb=" N   ILE B 822 " --> pdb=" O   ILE B 818 " (cutoff:3.500A)
      removed outlier: 3.700A  pdb=" N   GLY B 827 " --> pdb=" O   LEU B 823 " (cutoff:3.500A)
      removed outlier: 3.731A  pdb=" N   GLN B 832 " --> pdb=" O   LYS B 828 " (cutoff:3.500A)
      removed outlier: 4.119A  pdb=" N   LYS B 852 " --> pdb=" O   GLU B 848 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 853 through 858
      removed outlier: 3.539A  pdb=" N   MET B 857 " --> pdb=" O   ILE B 853 " (cutoff:3.500A)
      removed outlier: 3.640A  pdb=" N   VAL B 858 " --> pdb=" O   ILE B 854 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 853 through 858'
    Processing helix  chain 'B' and resid 860 through 889
      removed outlier: 3.568A  pdb=" N   LYS B 880 " --> pdb=" O   LEU B 876 " (cutoff:3.500A)
      removed outlier: 3.738A  pdb=" N   GLU B 881 " --> pdb=" O   GLN B 877 " (cutoff:3.500A)
      removed outlier: 3.742A  pdb=" N   HIS B 889 " --> pdb=" O   LEU B 885 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 890 through 919
      removed outlier: 3.533A  pdb=" N   VAL B 894 " --> pdb=" O   PRO B 890 " (cutoff:3.500A)
      removed outlier: 4.306A  pdb=" N   ILE B 902 " --> pdb=" O   THR B 898 " (cutoff:3.500A)
      removed outlier: 4.178A  pdb=" N   ARG B 903 " --> pdb=" O   ARG B 899 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 923 through 943
      removed outlier: 3.893A  pdb=" N   THR B 933 " --> pdb=" O   LYS B 929 " (cutoff:3.500A)
      removed outlier: 3.593A  pdb=" N   VAL B 934 " --> pdb=" O   LEU B 930 " (cutoff:3.500A)
      removed outlier: 3.814A  pdb=" N   ASN B 943 " --> pdb=" O   LYS B 939 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 954 through 962
      removed outlier: 4.042A  pdb=" N   TRP B 962 " --> pdb=" O   LYS B 958 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 966 through 975
    Processing helix  chain 'B' and resid 1044 through 1049
    Processing helix  chain 'B' and resid 1070 through 1080
      removed outlier: 3.600A  pdb=" N   PHE B1080 " --> pdb=" O   ALA B1076 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1084 through 1100
    Processing helix  chain 'B' and resid 1100 through 1105
      removed outlier: 3.848A  pdb=" N   MET B1104 " --> pdb=" O   THR B1100 " (cutoff:3.500A)
      removed outlier: 4.101A  pdb=" N   GLU B1105 " --> pdb=" O   PRO B1101 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 1100 through 1105'
    Processing helix  chain 'B' and resid 1113 through 1121
    Processing sheet with id=AA1, first strand: chain 'A' and resid 980 through 982
      removed outlier: 6.500A  pdb=" N   TYR A1066 " --> pdb=" O   ILE A1001 " (cutoff:3.500A)
      removed outlier: 5.717A  pdb=" N   ILE A1001 " --> pdb=" O   TYR A1066 " (cutoff:3.500A)
      removed outlier: 7.406A  pdb=" N   ILE A1068 " --> pdb=" O   PHE A 999 " (cutoff:3.500A)
      removed outlier: 5.167A  pdb=" N   PHE A 999 " --> pdb=" O   ILE A1068 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 987 through 989
      removed outlier: 6.682A  pdb=" N   VAL A 987 " --> pdb=" O   CYS A1059 " (cutoff:3.500A)
      removed outlier: 7.610A  pdb=" N   CYS A1059 " --> pdb=" O   VAL A 987 " (cutoff:3.500A)
      removed outlier: 4.355A  pdb=" N   VAL A 989 " --> pdb=" O   VAL A1057 " (cutoff:3.500A)
      removed outlier: 4.019A  pdb=" N   VAL A1057 " --> pdb=" O   VAL A 989 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 1124 through 1126
      removed outlier: 6.815A  pdb=" N   PHE A1187 " --> pdb=" O   LEU A1147 " (cutoff:3.500A)
      removed outlier: 5.613A  pdb=" N   LEU A1147 " --> pdb=" O   PHE A1187 " (cutoff:3.500A)
      removed outlier: 7.518A  pdb=" N   VAL A1189 " --> pdb=" O   VAL A1145 " (cutoff:3.500A)
      removed outlier: 5.600A  pdb=" N   VAL A1145 " --> pdb=" O   VAL A1189 " (cutoff:3.500A)
      removed outlier: 4.039A  pdb=" N   LEU A1147 " --> pdb=" O   CYS A1165 " (cutoff:3.500A)
      removed outlier: 4.637A  pdb=" N   CYS A1165 " --> pdb=" O   LEU A1147 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 1135 through 1137
    Processing sheet with id=AA5, first strand: chain 'B' and resid 980 through 982
      removed outlier: 6.477A  pdb=" N   TYR B1066 " --> pdb=" O   ILE B1001 " (cutoff:3.500A)
      removed outlier: 5.788A  pdb=" N   ILE B1001 " --> pdb=" O   TYR B1066 " (cutoff:3.500A)
      removed outlier: 7.478A  pdb=" N   ILE B1068 " --> pdb=" O   PHE B 999 " (cutoff:3.500A)
      removed outlier: 5.198A  pdb=" N   PHE B 999 " --> pdb=" O   ILE B1068 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 987 through 989
      removed outlier: 3.888A  pdb=" N   ILE B 988 " --> pdb=" O   VAL B1057 " (cutoff:3.500A)
      removed outlier: 7.881A  pdb=" N   VAL B1057 " --> pdb=" O   ILE B 988 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 1124 through 1126
      removed outlier: 6.041A  pdb=" N   ARG B1185 " --> pdb=" O   ILE B1148 " (cutoff:3.500A)
      removed outlier: 4.158A  pdb=" N   LEU B1147 " --> pdb=" O   CYS B1165 " (cutoff:3.500A)
      removed outlier: 4.720A  pdb=" N   CYS B1165 " --> pdb=" O   LEU B1147 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 1135 through 1137

    1067 hydrogen bonds defined for protein.
    3171 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 5.30

  Time building geometry restraints manager: 5.24 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 2544
        1.33 -     1.45: 3738
        1.45 -     1.57: 8830
        1.57 -     1.69: 8
        1.69 -     1.81: 118
  Bond restraints: 15238
  Sorted by residual:
  bond pdb=" C26 AJP B1404 "
       pdb=" O25 AJP B1404 "
    ideal  model  delta    sigma   weight residual
    1.375  1.413 -0.038 2.00e-02 2.50e+03 3.59e+00
  bond pdb=" C26 AJP B1403 "
       pdb=" O25 AJP B1403 "
    ideal  model  delta    sigma   weight residual
    1.375  1.412 -0.037 2.00e-02 2.50e+03 3.47e+00
  bond pdb=" C26 AJP B1405 "
       pdb=" O25 AJP B1405 "
    ideal  model  delta    sigma   weight residual
    1.375  1.412 -0.037 2.00e-02 2.50e+03 3.45e+00
  bond pdb=" C45 AJP B1404 "
       pdb=" O44 AJP B1404 "
    ideal  model  delta    sigma   weight residual
    1.375  1.410 -0.035 2.00e-02 2.50e+03 3.14e+00
  bond pdb=" C45 AJP B1405 "
       pdb=" O44 AJP B1405 "
    ideal  model  delta    sigma   weight residual
    1.375  1.410 -0.035 2.00e-02 2.50e+03 3.03e+00
  ... (remaining 15233 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.06: 20463
        2.06 -     4.13: 291
        4.13 -     6.19: 49
        6.19 -     8.26: 12
        8.26 -    10.32: 5
  Bond angle restraints: 20820
  Sorted by residual:
  angle pdb=" O1P CMP B1406 "
        pdb=" P   CMP B1406 "
        pdb=" O2P CMP B1406 "
      ideal   model   delta    sigma   weight residual
     109.50  118.76   -9.26 3.00e+00 1.11e-01 9.53e+00
  angle pdb=" O1P CMP A1403 "
        pdb=" P   CMP A1403 "
        pdb=" O2P CMP A1403 "
      ideal   model   delta    sigma   weight residual
     109.50  118.75   -9.25 3.00e+00 1.11e-01 9.52e+00
  angle pdb=" C   PHE B 294 "
        pdb=" N   ASN B 295 "
        pdb=" CA  ASN B 295 "
      ideal   model   delta    sigma   weight residual
     121.54  127.23   -5.69 1.91e+00 2.74e-01 8.88e+00
  angle pdb=" C   PHE A 294 "
        pdb=" N   ASN A 295 "
        pdb=" CA  ASN A 295 "
      ideal   model   delta    sigma   weight residual
     121.54  127.21   -5.67 1.91e+00 2.74e-01 8.81e+00
  angle pdb=" CA  LEU B 979 "
        pdb=" CB  LEU B 979 "
        pdb=" CG  LEU B 979 "
      ideal   model   delta    sigma   weight residual
     116.30  126.62  -10.32 3.50e+00 8.16e-02 8.70e+00
  ... (remaining 20815 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    26.19: 9076
       26.19 -    52.37: 359
       52.37 -    78.56: 53
       78.56 -   104.74: 35
      104.74 -   130.93: 91
  Dihedral angle restraints: 9614
    sinusoidal: 3926
      harmonic: 5688
  Sorted by residual:
  dihedral pdb=" O31 AJP B1404 "
           pdb=" C30 AJP B1404 "
           pdb=" C32 AJP B1404 "
           pdb=" O33 AJP B1404 "
      ideal   model   delta sinusoidal    sigma   weight residual
     177.28   52.81  124.47     1      3.00e+01 1.11e-03 1.67e+01
  dihedral pdb=" C45 AJP A1402 "
           pdb=" C49 AJP A1402 "
           pdb=" O50 AJP A1402 "
           pdb=" C48 AJP A1402 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -62.82   61.40 -124.22     1      3.00e+01 1.11e-03 1.67e+01
  dihedral pdb=" C46 AJP A1402 "
           pdb=" C45 AJP A1402 "
           pdb=" O50 AJP A1402 "
           pdb=" C49 AJP A1402 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -62.83   60.12 -122.95     1      3.00e+01 1.11e-03 1.65e+01
  ... (remaining 9611 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.048: 2015
       0.048 -    0.097: 494
       0.097 -    0.145: 75
       0.145 -    0.194: 6
       0.194 -    0.242: 9
  Chirality restraints: 2599
  Sorted by residual:
  chirality pdb=" C22 AJP B1404 "
            pdb=" C21 AJP B1404 "
            pdb=" C23 AJP B1404 "
            pdb=" O79 AJP B1404 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.47    2.23    0.24 2.00e-01 2.50e+01 1.47e+00
  chirality pdb=" C10 AJP B1403 "
            pdb=" C08 AJP B1403 "
            pdb=" C11 AJP B1403 "
            pdb=" O82 AJP B1403 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.61    2.38    0.23 2.00e-01 2.50e+01 1.31e+00
  chirality pdb=" C10 AJP B1404 "
            pdb=" C08 AJP B1404 "
            pdb=" C11 AJP B1404 "
            pdb=" O82 AJP B1404 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.61    2.38    0.23 2.00e-01 2.50e+01 1.31e+00
  ... (remaining 2596 not shown)

  Planarity restraints: 2529
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU B 138 "    0.008 2.00e-02 2.50e+03   1.65e-02 2.72e+00
        pdb=" C   LEU B 138 "   -0.029 2.00e-02 2.50e+03
        pdb=" O   LEU B 138 "    0.011 2.00e-02 2.50e+03
        pdb=" N   LEU B 139 "    0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU A 138 "   -0.008 2.00e-02 2.50e+03   1.64e-02 2.70e+00
        pdb=" C   LEU A 138 "    0.028 2.00e-02 2.50e+03
        pdb=" O   LEU A 138 "   -0.011 2.00e-02 2.50e+03
        pdb=" N   LEU A 139 "   -0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA A 944 "    0.026 5.00e-02 4.00e+02   3.94e-02 2.48e+00
        pdb=" N   PRO A 945 "   -0.068 5.00e-02 4.00e+02
        pdb=" CA  PRO A 945 "    0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO A 945 "    0.022 5.00e-02 4.00e+02
  ... (remaining 2526 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.75: 1768
        2.75 -     3.29: 15040
        3.29 -     3.83: 24475
        3.83 -     4.36: 24606
        4.36 -     4.90: 44195
  Nonbonded interactions: 110084
  Sorted by model distance:
  nonbonded pdb=" O62 AJP B1403 "
            pdb=" O63 AJP B1403 "
     model   vdw
     2.218 3.040
  nonbonded pdb=" O42 AJP A1402 "
            pdb=" O52 AJP A1402 "
     model   vdw
     2.268 3.040
  nonbonded pdb=" O32 POV B1402 "
            pdb=" O79 AJP B1405 "
     model   vdw
     2.270 3.040
  nonbonded pdb=" O32 POV A1401 "
            pdb=" O79 AJP B1403 "
     model   vdw
     2.306 3.040
  nonbonded pdb=" OG1 THR B 208 "
            pdb=" O   LEU B 430 "
     model   vdw
     2.319 3.040
  ... (remaining 110079 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
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 76 through 382 or (resid 383 and (name N or name CA or nam \ 
e C or name O or name CB )) or resid 384 through 652 or resid 678 through 690 or \ 
 (resid 691 through 693 and (name N or name CA or name C or name O or name CB )) \ 
 or resid 694 through 1076 or (resid 1077 through 1079 and (name N or name CA or \ 
 name C or name O or name CB )) or resid 1080 through 1190 or resid 1402 through \ 
 1403))
  selection = (chain 'B' and (resid 76 through 216 or (resid 217 and (name N or name CA or nam \ 
e C or name O or name CB )) or resid 218 through 610 or (resid 611 and (name N o \ 
r name CA or name C or name O or name CB )) or resid 612 through 885 or (resid 8 \ 
86 and (name N or name CA or name C or name O or name CB )) or resid 887 through \ 
 1190 or resid 1405 through 1406))
}

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:             0.270
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.610
  Check model and map are aligned:         0.120
  Set scattering table:                    0.150
  Process input model:                     36.990
  Find NCS groups from input model:        0.730
  Set up NCS constraints:                  0.070
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.670
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   41.620
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7771
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      :  0.003   0.038  15238  Z= 0.173
  Angle     :  0.646  10.323  20820  Z= 0.319
  Chirality :  0.043   0.242   2599
  Planarity :  0.004   0.039   2529
  Dihedral  : 20.602 130.930   5924
  Min Nonbonded Distance : 2.218

Molprobity Statistics.
  All-atom Clashscore : 5.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.71 %
    Favored  : 98.29 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 11.80 %
    Favored  : 88.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.09 (0.19), residues: 1935
  helix:  1.21 (0.14), residues: 1357
  sheet:  1.70 (0.52), residues: 105
  loop : -0.77 (0.27), residues: 473

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP B 635 
 HIS   0.002   0.001   HIS A 908 
 PHE   0.010   0.001   PHE B1080 
 TYR   0.022   0.001   TYR B 309 
 ARG   0.002   0.000   ARG B 573 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.10752 ( 1067)
  hydrogen bonds       : angle       4.59147 ( 3171)
  covalent geometry    : bond        0.00317 (15238)
  covalent geometry    : angle       0.64576 (20820)

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

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

  3870 Ramachandran restraints generated.
    1935 Oldfield, 0 Emsley, 1935 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3870 Ramachandran restraints generated.
    1935 Oldfield, 0 Emsley, 1935 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  249 residues out of total 1682 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 249
  time to evaluate  : 1.541 
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: A  249 MET cc_start: 0.8200 (tmm) cc_final: 0.7832 (tmm)
REVERT: A  277 LEU cc_start: 0.8755 (tp) cc_final: 0.8453 (mm)
REVERT: A  383 MET cc_start: 0.6424 (ttt) cc_final: 0.6069 (tpp)
REVERT: A  397 ILE cc_start: 0.9254 (pt) cc_final: 0.8986 (pt)
REVERT: A  398 ILE cc_start: 0.8954 (pt) cc_final: 0.8749 (pt)
REVERT: A  503 GLU cc_start: 0.7983 (tm-30) cc_final: 0.7749 (tm-30)
REVERT: A  926 GLU cc_start: 0.8294 (mp0) cc_final: 0.7493 (mp0)
REVERT: B  231 GLU cc_start: 0.7814 (mt-10) cc_final: 0.7574 (mt-10)
REVERT: B  397 ILE cc_start: 0.9299 (pt) cc_final: 0.9025 (pt)
REVERT: B  398 ILE cc_start: 0.8979 (pt) cc_final: 0.8776 (pt)
REVERT: B  503 GLU cc_start: 0.7963 (tm-30) cc_final: 0.7718 (tm-30)
REVERT: B  938 MET cc_start: 0.8589 (tpp) cc_final: 0.8034 (tpp)
  outliers start: 0
  outliers final: 0
  residues processed: 249
  average time/residue: 0.2166
  time to fit residues: 83.9334
Evaluate side-chains
  175 residues out of total 1682 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 175
  time to evaluate  : 1.544 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 195
   random chunks:
   chunk 164 optimal weight:    0.9980
   chunk 147 optimal weight:    2.9990
   chunk 82 optimal weight:   40.0000
   chunk 50 optimal weight:    1.9990
   chunk 99 optimal weight:    8.9990
   chunk 78 optimal weight:    9.9990
   chunk 152 optimal weight:   20.0000
   chunk 59 optimal weight:    0.4980
   chunk 92 optimal weight:   50.0000
   chunk 113 optimal weight:    0.9990
   chunk 177 optimal weight:   30.0000
   overall best weight:    1.4986

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

Flipped N/Q/H residues before XYZ refinement:
A 187 ASN
A 270 GLN
** A 597 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 900 GLN
** B 597 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 900 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4076 r_free = 0.4076 target = 0.150492 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3537 r_free = 0.3537 target = 0.109951 restraints weight = 29620.699|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3499 r_free = 0.3499 target = 0.108865 restraints weight = 37302.762|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3514 r_free = 0.3514 target = 0.110088 restraints weight = 23971.168|
|-----------------------------------------------------------------------------|
r_work (final): 0.3512
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7822
moved from start:          0.1222

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029  15238  Z= 0.143
  Angle     :  0.711   9.786  20820  Z= 0.325
  Chirality :  0.042   0.252   2599
  Planarity :  0.003   0.037   2529
  Dihedral  : 16.692 136.430   2956
  Min Nonbonded Distance : 2.432

Molprobity Statistics.
  All-atom Clashscore : 5.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.38 %
    Favored  : 97.62 %
  Rotamer:
    Outliers :  1.85 %
    Allowed  : 14.29 %
    Favored  : 83.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.81 (0.19), residues: 1935
  helix:  1.79 (0.14), residues: 1377
  sheet:  1.58 (0.51), residues: 107
  loop : -0.69 (0.28), residues: 451

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.033   0.001   TRP B1091 
 HIS   0.003   0.001   HIS A 132 
 PHE   0.020   0.001   PHE A 386 
 TYR   0.022   0.001   TYR A 309 
 ARG   0.003   0.000   ARG B 585 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04633 ( 1067)
  hydrogen bonds       : angle       3.90539 ( 3171)
  covalent geometry    : bond        0.00302 (15238)
  covalent geometry    : angle       0.71123 (20820)

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

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

  3870 Ramachandran restraints generated.
    1935 Oldfield, 0 Emsley, 1935 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3870 Ramachandran restraints generated.
    1935 Oldfield, 0 Emsley, 1935 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  223 residues out of total 1682 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 197
  time to evaluate  : 1.714 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  249 MET cc_start: 0.8226 (tmm) cc_final: 0.7921 (tmm)
REVERT: A  277 LEU cc_start: 0.8865 (tp) cc_final: 0.8525 (mm)
REVERT: A  926 GLU cc_start: 0.8471 (mp0) cc_final: 0.7611 (mp0)
REVERT: B  187 ASN cc_start: 0.7601 (m-40) cc_final: 0.7206 (m-40)
REVERT: B  195 PHE cc_start: 0.8256 (t80) cc_final: 0.7929 (t80)
REVERT: B  388 LEU cc_start: 0.9533 (OUTLIER) cc_final: 0.9311 (tt)
REVERT: B  389 ILE cc_start: 0.9177 (OUTLIER) cc_final: 0.8893 (mp)
REVERT: B  823 LEU cc_start: 0.9154 (mt) cc_final: 0.8949 (pp)
REVERT: B  938 MET cc_start: 0.8412 (tpp) cc_final: 0.7933 (tpp)
  outliers start: 26
  outliers final: 6
  residues processed: 218
  average time/residue: 0.2009
  time to fit residues: 71.1063
Evaluate side-chains
  181 residues out of total 1682 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 173
  time to evaluate  : 1.549 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   84 SER
Chi-restraints excluded: chain A residue  184 LEU
Chi-restraints excluded: chain A residue  464 VAL
Chi-restraints excluded: chain A residue 1006 VAL
Chi-restraints excluded: chain B residue   84 SER
Chi-restraints excluded: chain B residue  277 LEU
Chi-restraints excluded: chain B residue  388 LEU
Chi-restraints excluded: chain B residue  389 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 195
   random chunks:
   chunk 136 optimal weight:    0.8980
   chunk 113 optimal weight:    0.8980
   chunk 157 optimal weight:   50.0000
   chunk 183 optimal weight:   40.0000
   chunk 107 optimal weight:    1.9990
   chunk 190 optimal weight:   50.0000
   chunk 185 optimal weight:    7.9990
   chunk 189 optimal weight:   50.0000
   chunk 112 optimal weight:    1.9990
   chunk 9 optimal weight:    2.9990
   chunk 29 optimal weight:    0.9990
   overall best weight:    1.3586

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

Flipped N/Q/H residues before XYZ refinement:
** A 597 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 900 GLN
** B 597 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 900 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4074 r_free = 0.4074 target = 0.150513 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3425 r_free = 0.3425 target = 0.103467 restraints weight = 29570.700|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3367 r_free = 0.3367 target = 0.101309 restraints weight = 20316.649|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3374 r_free = 0.3374 target = 0.101904 restraints weight = 17495.065|
|-----------------------------------------------------------------------------|
r_work (final): 0.3350
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8037
moved from start:          0.1449

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  15238  Z= 0.130
  Angle     :  0.666  11.247  20820  Z= 0.306
  Chirality :  0.041   0.278   2599
  Planarity :  0.003   0.032   2529
  Dihedral  : 13.061 135.514   2956
  Min Nonbonded Distance : 2.385

Molprobity Statistics.
  All-atom Clashscore : 5.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.07 %
    Favored  : 97.93 %
  Rotamer:
    Outliers :  3.06 %
    Allowed  : 15.28 %
    Favored  : 81.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.06 (0.19), residues: 1935
  helix:  2.00 (0.14), residues: 1370
  sheet:  1.56 (0.50), residues: 107
  loop : -0.64 (0.28), residues: 458

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.032   0.001   TRP A1091 
 HIS   0.003   0.000   HIS A 889 
 PHE   0.011   0.001   PHE A 352 
 TYR   0.020   0.001   TYR B 309 
 ARG   0.004   0.000   ARG B 573 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04459 ( 1067)
  hydrogen bonds       : angle       3.76812 ( 3171)
  covalent geometry    : bond        0.00274 (15238)
  covalent geometry    : angle       0.66588 (20820)

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

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

  3870 Ramachandran restraints generated.
    1935 Oldfield, 0 Emsley, 1935 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3870 Ramachandran restraints generated.
    1935 Oldfield, 0 Emsley, 1935 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  228 residues out of total 1682 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 185
  time to evaluate  : 1.607 
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: A  249 MET cc_start: 0.8408 (tmm) cc_final: 0.8100 (tmm)
REVERT: A  277 LEU cc_start: 0.8896 (tp) cc_final: 0.8565 (mm)
REVERT: A  383 MET cc_start: 0.8162 (tpp) cc_final: 0.7868 (ttt)
REVERT: A  494 MET cc_start: 0.8718 (tpp) cc_final: 0.8212 (tpp)
REVERT: A  926 GLU cc_start: 0.8512 (mp0) cc_final: 0.7627 (mp0)
REVERT: B  187 ASN cc_start: 0.7557 (m-40) cc_final: 0.7333 (m-40)
REVERT: B  199 MET cc_start: 0.8535 (tpp) cc_final: 0.8201 (tpt)
REVERT: B  388 LEU cc_start: 0.9531 (OUTLIER) cc_final: 0.9322 (tt)
REVERT: B  389 ILE cc_start: 0.9352 (OUTLIER) cc_final: 0.9125 (mp)
REVERT: B  494 MET cc_start: 0.8750 (tpp) cc_final: 0.8248 (tpp)
REVERT: B  624 GLN cc_start: 0.8541 (tp-100) cc_final: 0.8249 (pm20)
REVERT: B  823 LEU cc_start: 0.9291 (mt) cc_final: 0.9063 (pp)
  outliers start: 43
  outliers final: 18
  residues processed: 218
  average time/residue: 0.1998
  time to fit residues: 71.1920
Evaluate side-chains
  190 residues out of total 1682 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 170
  time to evaluate  : 1.508 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   84 SER
Chi-restraints excluded: chain A residue  107 LEU
Chi-restraints excluded: chain A residue  184 LEU
Chi-restraints excluded: chain A residue  402 VAL
Chi-restraints excluded: chain A residue  464 VAL
Chi-restraints excluded: chain A residue  858 VAL
Chi-restraints excluded: chain A residue 1006 VAL
Chi-restraints excluded: chain A residue 1188 VAL
Chi-restraints excluded: chain B residue   84 SER
Chi-restraints excluded: chain B residue  107 LEU
Chi-restraints excluded: chain B residue  242 ILE
Chi-restraints excluded: chain B residue  277 LEU
Chi-restraints excluded: chain B residue  310 LEU
Chi-restraints excluded: chain B residue  319 LEU
Chi-restraints excluded: chain B residue  388 LEU
Chi-restraints excluded: chain B residue  389 ILE
Chi-restraints excluded: chain B residue  390 ILE
Chi-restraints excluded: chain B residue  402 VAL
Chi-restraints excluded: chain B residue  822 ILE
Chi-restraints excluded: chain B residue  858 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 195
   random chunks:
   chunk 89 optimal weight:    6.9990
   chunk 184 optimal weight:   20.0000
   chunk 123 optimal weight:    6.9990
   chunk 104 optimal weight:    0.6980
   chunk 180 optimal weight:   20.0000
   chunk 172 optimal weight:    5.9990
   chunk 66 optimal weight:    2.9990
   chunk 149 optimal weight:    3.9990
   chunk 21 optimal weight:    2.9990
   chunk 4 optimal weight:    9.9990
   chunk 161 optimal weight:    4.9990
   overall best weight:    3.1388

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

Flipped N/Q/H residues before XYZ refinement:
A 165 GLN
** A 597 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 900 GLN
** B 597 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 900 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4033 r_free = 0.4033 target = 0.147313 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3325 r_free = 0.3325 target = 0.098127 restraints weight = 29741.978|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3270 r_free = 0.3270 target = 0.095491 restraints weight = 20343.610|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3274 r_free = 0.3274 target = 0.095899 restraints weight = 17437.468|
|-----------------------------------------------------------------------------|
r_work (final): 0.3258
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8151
moved from start:          0.1800

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.045  15238  Z= 0.199
  Angle     :  0.692   9.670  20820  Z= 0.330
  Chirality :  0.042   0.297   2599
  Planarity :  0.003   0.033   2529
  Dihedral  : 11.064 135.490   2956
  Min Nonbonded Distance : 2.349

Molprobity Statistics.
  All-atom Clashscore : 7.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.33 %
    Favored  : 97.67 %
  Rotamer:
    Outliers :  3.34 %
    Allowed  : 16.70 %
    Favored  : 79.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.01 (0.19), residues: 1935
  helix:  1.94 (0.14), residues: 1371
  sheet:  1.53 (0.50), residues: 107
  loop : -0.56 (0.29), residues: 457

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.052   0.002   TRP A1091 
 HIS   0.004   0.001   HIS A 889 
 PHE   0.017   0.001   PHE A 352 
 TYR   0.025   0.001   TYR B 309 
 ARG   0.004   0.000   ARG A 585 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05239 ( 1067)
  hydrogen bonds       : angle       3.88211 ( 3171)
  covalent geometry    : bond        0.00459 (15238)
  covalent geometry    : angle       0.69167 (20820)

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

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

  3870 Ramachandran restraints generated.
    1935 Oldfield, 0 Emsley, 1935 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3870 Ramachandran restraints generated.
    1935 Oldfield, 0 Emsley, 1935 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  230 residues out of total 1682 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 183
  time to evaluate  : 1.734 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  195 PHE cc_start: 0.8266 (t80) cc_final: 0.8019 (t80)
REVERT: A  249 MET cc_start: 0.8470 (tmm) cc_final: 0.8072 (tmm)
REVERT: A  354 GLU cc_start: 0.7794 (mm-30) cc_final: 0.7476 (mp0)
REVERT: A  383 MET cc_start: 0.8149 (tpp) cc_final: 0.7921 (ttt)
REVERT: A  388 LEU cc_start: 0.9550 (OUTLIER) cc_final: 0.9327 (tt)
REVERT: A  494 MET cc_start: 0.8754 (tpp) cc_final: 0.8281 (tpp)
REVERT: A  926 GLU cc_start: 0.8589 (mp0) cc_final: 0.7665 (mp0)
REVERT: B  187 ASN cc_start: 0.7535 (m-40) cc_final: 0.7153 (m110)
REVERT: B  388 LEU cc_start: 0.9563 (OUTLIER) cc_final: 0.9317 (tt)
REVERT: B  389 ILE cc_start: 0.9394 (OUTLIER) cc_final: 0.9124 (mp)
REVERT: B  494 MET cc_start: 0.8730 (tpp) cc_final: 0.8243 (tpp)
REVERT: B  624 GLN cc_start: 0.8604 (tp-100) cc_final: 0.8263 (pm20)
REVERT: B  823 LEU cc_start: 0.9296 (mt) cc_final: 0.8976 (pp)
REVERT: B  848 GLU cc_start: 0.8311 (tp30) cc_final: 0.8085 (tp30)
  outliers start: 47
  outliers final: 30
  residues processed: 220
  average time/residue: 0.1968
  time to fit residues: 71.0196
Evaluate side-chains
  203 residues out of total 1682 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 170
  time to evaluate  : 1.568 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   79 VAL
Chi-restraints excluded: chain A residue   84 SER
Chi-restraints excluded: chain A residue  107 LEU
Chi-restraints excluded: chain A residue  282 VAL
Chi-restraints excluded: chain A residue  310 LEU
Chi-restraints excluded: chain A residue  373 THR
Chi-restraints excluded: chain A residue  388 LEU
Chi-restraints excluded: chain A residue  402 VAL
Chi-restraints excluded: chain A residue  464 VAL
Chi-restraints excluded: chain A residue  477 LEU
Chi-restraints excluded: chain A residue  587 LEU
Chi-restraints excluded: chain A residue  844 ILE
Chi-restraints excluded: chain A residue  858 VAL
Chi-restraints excluded: chain A residue 1006 VAL
Chi-restraints excluded: chain A residue 1188 VAL
Chi-restraints excluded: chain B residue   84 SER
Chi-restraints excluded: chain B residue  107 LEU
Chi-restraints excluded: chain B residue  133 MET
Chi-restraints excluded: chain B residue  242 ILE
Chi-restraints excluded: chain B residue  277 LEU
Chi-restraints excluded: chain B residue  282 VAL
Chi-restraints excluded: chain B residue  310 LEU
Chi-restraints excluded: chain B residue  319 LEU
Chi-restraints excluded: chain B residue  341 ILE
Chi-restraints excluded: chain B residue  373 THR
Chi-restraints excluded: chain B residue  388 LEU
Chi-restraints excluded: chain B residue  389 ILE
Chi-restraints excluded: chain B residue  390 ILE
Chi-restraints excluded: chain B residue  402 VAL
Chi-restraints excluded: chain B residue  464 VAL
Chi-restraints excluded: chain B residue  477 LEU
Chi-restraints excluded: chain B residue  822 ILE
Chi-restraints excluded: chain B residue  858 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 195
   random chunks:
   chunk 29 optimal weight:    0.7980
   chunk 89 optimal weight:    0.7980
   chunk 105 optimal weight:    7.9990
   chunk 6 optimal weight:    2.9990
   chunk 30 optimal weight:    3.9990
   chunk 59 optimal weight:   10.0000
   chunk 124 optimal weight:    0.9980
   chunk 68 optimal weight:    6.9990
   chunk 107 optimal weight:    1.9990
   chunk 113 optimal weight:    0.9990
   chunk 56 optimal weight:    3.9990
   overall best weight:    1.1184

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

Flipped N/Q/H residues before XYZ refinement:
A 165 GLN
** A 597 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 900 GLN
** B 597 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 900 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4062 r_free = 0.4062 target = 0.149675 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3409 r_free = 0.3409 target = 0.102394 restraints weight = 29845.579|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3340 r_free = 0.3340 target = 0.099861 restraints weight = 20118.534|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3353 r_free = 0.3353 target = 0.100696 restraints weight = 18563.161|
|-----------------------------------------------------------------------------|
r_work (final): 0.3345
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8050
moved from start:          0.1804

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050  15238  Z= 0.126
  Angle     :  0.623   9.906  20820  Z= 0.298
  Chirality :  0.039   0.188   2599
  Planarity :  0.003   0.033   2529
  Dihedral  : 10.114 135.236   2956
  Min Nonbonded Distance : 2.381

Molprobity Statistics.
  All-atom Clashscore : 7.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.96 %
    Favored  : 98.04 %
  Rotamer:
    Outliers :  2.84 %
    Allowed  : 17.91 %
    Favored  : 79.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.18 (0.19), residues: 1935
  helix:  2.10 (0.14), residues: 1369
  sheet:  1.59 (0.50), residues: 107
  loop : -0.61 (0.29), residues: 459

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.001   TRP A1091 
 HIS   0.002   0.000   HIS A 889 
 PHE   0.010   0.001   PHE A 268 
 TYR   0.021   0.001   TYR B 309 
 ARG   0.003   0.000   ARG A 940 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04583 ( 1067)
  hydrogen bonds       : angle       3.69302 ( 3171)
  covalent geometry    : bond        0.00265 (15238)
  covalent geometry    : angle       0.62318 (20820)

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

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

  3870 Ramachandran restraints generated.
    1935 Oldfield, 0 Emsley, 1935 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3870 Ramachandran restraints generated.
    1935 Oldfield, 0 Emsley, 1935 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  221 residues out of total 1682 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 181
  time to evaluate  : 1.636 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  187 ASN cc_start: 0.7635 (m110) cc_final: 0.7374 (m-40)
REVERT: A  195 PHE cc_start: 0.8166 (t80) cc_final: 0.7548 (t80)
REVERT: A  249 MET cc_start: 0.8454 (tmm) cc_final: 0.8113 (tmm)
REVERT: A  277 LEU cc_start: 0.8889 (tp) cc_final: 0.8503 (mm)
REVERT: A  354 GLU cc_start: 0.7466 (mm-30) cc_final: 0.7051 (mp0)
REVERT: A  494 MET cc_start: 0.8655 (tpp) cc_final: 0.8152 (tpp)
REVERT: A  926 GLU cc_start: 0.8500 (mp0) cc_final: 0.7560 (mp0)
REVERT: B  187 ASN cc_start: 0.7562 (m-40) cc_final: 0.7320 (m-40)
REVERT: B  388 LEU cc_start: 0.9527 (OUTLIER) cc_final: 0.9286 (tt)
REVERT: B  389 ILE cc_start: 0.9323 (OUTLIER) cc_final: 0.9097 (mp)
REVERT: B  494 MET cc_start: 0.8670 (tpp) cc_final: 0.8132 (tpp)
REVERT: B  823 LEU cc_start: 0.9292 (mt) cc_final: 0.8969 (pp)
  outliers start: 40
  outliers final: 28
  residues processed: 210
  average time/residue: 0.2004
  time to fit residues: 69.0739
Evaluate side-chains
  200 residues out of total 1682 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 170
  time to evaluate  : 1.561 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   79 VAL
Chi-restraints excluded: chain A residue   84 SER
Chi-restraints excluded: chain A residue  107 LEU
Chi-restraints excluded: chain A residue  184 LEU
Chi-restraints excluded: chain A residue  310 LEU
Chi-restraints excluded: chain A residue  402 VAL
Chi-restraints excluded: chain A residue  464 VAL
Chi-restraints excluded: chain A residue  477 LEU
Chi-restraints excluded: chain A residue  587 LEU
Chi-restraints excluded: chain A residue  844 ILE
Chi-restraints excluded: chain A residue  858 VAL
Chi-restraints excluded: chain A residue 1006 VAL
Chi-restraints excluded: chain A residue 1188 VAL
Chi-restraints excluded: chain B residue   78 ILE
Chi-restraints excluded: chain B residue   84 SER
Chi-restraints excluded: chain B residue  107 LEU
Chi-restraints excluded: chain B residue  133 MET
Chi-restraints excluded: chain B residue  242 ILE
Chi-restraints excluded: chain B residue  277 LEU
Chi-restraints excluded: chain B residue  310 LEU
Chi-restraints excluded: chain B residue  319 LEU
Chi-restraints excluded: chain B residue  388 LEU
Chi-restraints excluded: chain B residue  389 ILE
Chi-restraints excluded: chain B residue  390 ILE
Chi-restraints excluded: chain B residue  402 VAL
Chi-restraints excluded: chain B residue  464 VAL
Chi-restraints excluded: chain B residue  477 LEU
Chi-restraints excluded: chain B residue  587 LEU
Chi-restraints excluded: chain B residue  822 ILE
Chi-restraints excluded: chain B residue  858 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 195
   random chunks:
   chunk 7 optimal weight:    0.7980
   chunk 99 optimal weight:    4.9990
   chunk 45 optimal weight:    0.0170
   chunk 169 optimal weight:    6.9990
   chunk 170 optimal weight:    0.9980
   chunk 190 optimal weight:   50.0000
   chunk 8 optimal weight:    7.9990
   chunk 156 optimal weight:    0.0050
   chunk 13 optimal weight:    0.8980
   chunk 21 optimal weight:    1.9990
   chunk 148 optimal weight:    3.9990
   overall best weight:    0.5432

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

Flipped N/Q/H residues before XYZ refinement:
A 900 GLN
B 900 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4079 r_free = 0.4079 target = 0.150976 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3601 r_free = 0.3601 target = 0.113850 restraints weight = 29855.825|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3455 r_free = 0.3455 target = 0.108833 restraints weight = 35166.729|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3463 r_free = 0.3463 target = 0.109030 restraints weight = 33238.275|
|-----------------------------------------------------------------------------|
r_work (final): 0.3445
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7886
moved from start:          0.1840

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.045  15238  Z= 0.114
  Angle     :  0.604  10.442  20820  Z= 0.289
  Chirality :  0.039   0.199   2599
  Planarity :  0.003   0.031   2529
  Dihedral  :  9.495 135.006   2956
  Min Nonbonded Distance : 2.423

Molprobity Statistics.
  All-atom Clashscore : 6.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.86 %
    Favored  : 98.14 %
  Rotamer:
    Outliers :  2.63 %
    Allowed  : 19.12 %
    Favored  : 78.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.27 (0.19), residues: 1935
  helix:  2.16 (0.14), residues: 1367
  sheet:  1.61 (0.50), residues: 107
  loop : -0.55 (0.29), residues: 461

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.034   0.001   TRP A 962 
 HIS   0.001   0.000   HIS A 908 
 PHE   0.009   0.001   PHE A  95 
 TYR   0.019   0.001   TYR A 309 
 ARG   0.001   0.000   ARG A 585 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04171 ( 1067)
  hydrogen bonds       : angle       3.58902 ( 3171)
  covalent geometry    : bond        0.00229 (15238)
  covalent geometry    : angle       0.60394 (20820)

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

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

  3870 Ramachandran restraints generated.
    1935 Oldfield, 0 Emsley, 1935 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3870 Ramachandran restraints generated.
    1935 Oldfield, 0 Emsley, 1935 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  217 residues out of total 1682 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 180
  time to evaluate  : 1.695 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  187 ASN cc_start: 0.7442 (m110) cc_final: 0.7196 (m-40)
REVERT: A  195 PHE cc_start: 0.8049 (t80) cc_final: 0.7325 (t80)
REVERT: A  249 MET cc_start: 0.8315 (tmm) cc_final: 0.8014 (tmm)
REVERT: A  277 LEU cc_start: 0.8844 (tp) cc_final: 0.8480 (mm)
REVERT: A  494 MET cc_start: 0.8580 (tpp) cc_final: 0.8078 (tpp)
REVERT: A  926 GLU cc_start: 0.8580 (mp0) cc_final: 0.7631 (mp0)
REVERT: B  187 ASN cc_start: 0.7433 (m-40) cc_final: 0.7173 (m-40)
REVERT: B  388 LEU cc_start: 0.9531 (OUTLIER) cc_final: 0.9291 (tt)
REVERT: B  389 ILE cc_start: 0.9302 (OUTLIER) cc_final: 0.9060 (mp)
REVERT: B  494 MET cc_start: 0.8564 (tpp) cc_final: 0.8034 (tpp)
REVERT: B  823 LEU cc_start: 0.9316 (mt) cc_final: 0.8990 (pp)
  outliers start: 37
  outliers final: 24
  residues processed: 210
  average time/residue: 0.2026
  time to fit residues: 70.0735
Evaluate side-chains
  197 residues out of total 1682 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 171
  time to evaluate  : 1.679 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   84 SER
Chi-restraints excluded: chain A residue  184 LEU
Chi-restraints excluded: chain A residue  310 LEU
Chi-restraints excluded: chain A residue  373 THR
Chi-restraints excluded: chain A residue  464 VAL
Chi-restraints excluded: chain A residue  587 LEU
Chi-restraints excluded: chain A residue  844 ILE
Chi-restraints excluded: chain A residue  858 VAL
Chi-restraints excluded: chain A residue 1006 VAL
Chi-restraints excluded: chain A residue 1188 VAL
Chi-restraints excluded: chain B residue   78 ILE
Chi-restraints excluded: chain B residue   79 VAL
Chi-restraints excluded: chain B residue   84 SER
Chi-restraints excluded: chain B residue  133 MET
Chi-restraints excluded: chain B residue  162 SER
Chi-restraints excluded: chain B residue  277 LEU
Chi-restraints excluded: chain B residue  310 LEU
Chi-restraints excluded: chain B residue  319 LEU
Chi-restraints excluded: chain B residue  373 THR
Chi-restraints excluded: chain B residue  388 LEU
Chi-restraints excluded: chain B residue  389 ILE
Chi-restraints excluded: chain B residue  390 ILE
Chi-restraints excluded: chain B residue  464 VAL
Chi-restraints excluded: chain B residue  587 LEU
Chi-restraints excluded: chain B residue  822 ILE
Chi-restraints excluded: chain B residue  858 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 195
   random chunks:
   chunk 189 optimal weight:   50.0000
   chunk 130 optimal weight:    6.9990
   chunk 166 optimal weight:    4.9990
   chunk 91 optimal weight:    0.7980
   chunk 44 optimal weight:    1.9990
   chunk 133 optimal weight:    0.8980
   chunk 49 optimal weight:    1.9990
   chunk 2 optimal weight:   10.0000
   chunk 159 optimal weight:    0.9980
   chunk 136 optimal weight:    0.9980
   chunk 19 optimal weight:    5.9990
   overall best weight:    1.1382

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

Flipped N/Q/H residues before XYZ refinement:
** A 597 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 900 GLN
** B 597 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 900 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4074 r_free = 0.4074 target = 0.151158 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3420 r_free = 0.3420 target = 0.103849 restraints weight = 30051.587|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3366 r_free = 0.3366 target = 0.101774 restraints weight = 20726.075|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3370 r_free = 0.3370 target = 0.101966 restraints weight = 17230.236|
|-----------------------------------------------------------------------------|
r_work (final): 0.3346
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8028
moved from start:          0.1946

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  15238  Z= 0.121
  Angle     :  0.623  11.163  20820  Z= 0.297
  Chirality :  0.039   0.206   2599
  Planarity :  0.003   0.032   2529
  Dihedral  :  9.285 134.851   2956
  Min Nonbonded Distance : 2.433

Molprobity Statistics.
  All-atom Clashscore : 6.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.86 %
    Favored  : 98.14 %
  Rotamer:
    Outliers :  2.77 %
    Allowed  : 19.76 %
    Favored  : 77.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.27 (0.19), residues: 1935
  helix:  2.14 (0.14), residues: 1373
  sheet:  1.60 (0.49), residues: 107
  loop : -0.49 (0.29), residues: 455

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.067   0.002   TRP A1091 
 HIS   0.002   0.000   HIS A 908 
 PHE   0.015   0.001   PHE A  95 
 TYR   0.020   0.001   TYR A 309 
 ARG   0.001   0.000   ARG A 585 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04187 ( 1067)
  hydrogen bonds       : angle       3.58931 ( 3171)
  covalent geometry    : bond        0.00260 (15238)
  covalent geometry    : angle       0.62287 (20820)

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

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

  3870 Ramachandran restraints generated.
    1935 Oldfield, 0 Emsley, 1935 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3870 Ramachandran restraints generated.
    1935 Oldfield, 0 Emsley, 1935 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  217 residues out of total 1682 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 178
  time to evaluate  : 1.565 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  195 PHE cc_start: 0.8116 (t80) cc_final: 0.7377 (t80)
REVERT: A  249 MET cc_start: 0.8389 (tmm) cc_final: 0.8068 (tmm)
REVERT: A  277 LEU cc_start: 0.8872 (tp) cc_final: 0.8488 (mm)
REVERT: A  354 GLU cc_start: 0.7394 (OUTLIER) cc_final: 0.7002 (mp0)
REVERT: A  494 MET cc_start: 0.8670 (tpp) cc_final: 0.8163 (tpp)
REVERT: A  926 GLU cc_start: 0.8580 (mp0) cc_final: 0.7567 (mp0)
REVERT: B  187 ASN cc_start: 0.7436 (m-40) cc_final: 0.7160 (m-40)
REVERT: B  388 LEU cc_start: 0.9498 (OUTLIER) cc_final: 0.9262 (tt)
REVERT: B  389 ILE cc_start: 0.9396 (OUTLIER) cc_final: 0.9162 (mp)
REVERT: B  494 MET cc_start: 0.8660 (tpp) cc_final: 0.8113 (tpp)
REVERT: B  823 LEU cc_start: 0.9280 (mt) cc_final: 0.8946 (pp)
  outliers start: 39
  outliers final: 28
  residues processed: 207
  average time/residue: 0.1948
  time to fit residues: 66.3922
Evaluate side-chains
  203 residues out of total 1682 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 172
  time to evaluate  : 1.672 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   79 VAL
Chi-restraints excluded: chain A residue   84 SER
Chi-restraints excluded: chain A residue  107 LEU
Chi-restraints excluded: chain A residue  184 LEU
Chi-restraints excluded: chain A residue  310 LEU
Chi-restraints excluded: chain A residue  354 GLU
Chi-restraints excluded: chain A residue  373 THR
Chi-restraints excluded: chain A residue  464 VAL
Chi-restraints excluded: chain A residue  587 LEU
Chi-restraints excluded: chain A residue  844 ILE
Chi-restraints excluded: chain A residue  858 VAL
Chi-restraints excluded: chain A residue 1006 VAL
Chi-restraints excluded: chain A residue 1091 TRP
Chi-restraints excluded: chain A residue 1188 VAL
Chi-restraints excluded: chain B residue   79 VAL
Chi-restraints excluded: chain B residue   84 SER
Chi-restraints excluded: chain B residue  107 LEU
Chi-restraints excluded: chain B residue  133 MET
Chi-restraints excluded: chain B residue  162 SER
Chi-restraints excluded: chain B residue  277 LEU
Chi-restraints excluded: chain B residue  310 LEU
Chi-restraints excluded: chain B residue  319 LEU
Chi-restraints excluded: chain B residue  373 THR
Chi-restraints excluded: chain B residue  388 LEU
Chi-restraints excluded: chain B residue  389 ILE
Chi-restraints excluded: chain B residue  390 ILE
Chi-restraints excluded: chain B residue  402 VAL
Chi-restraints excluded: chain B residue  464 VAL
Chi-restraints excluded: chain B residue  587 LEU
Chi-restraints excluded: chain B residue  822 ILE
Chi-restraints excluded: chain B residue  858 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 195
   random chunks:
   chunk 36 optimal weight:    0.6980
   chunk 113 optimal weight:    0.8980
   chunk 150 optimal weight:    3.9990
   chunk 176 optimal weight:    4.9990
   chunk 101 optimal weight:    5.9990
   chunk 90 optimal weight:   10.0000
   chunk 93 optimal weight:   20.0000
   chunk 170 optimal weight:    1.9990
   chunk 153 optimal weight:    5.9990
   chunk 182 optimal weight:   40.0000
   chunk 0 optimal weight:    5.9990
   overall best weight:    2.5186

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

Flipped N/Q/H residues before XYZ refinement:
A 165 GLN
A 187 ASN
** A 597 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 900 GLN
** B 597 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 900 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4051 r_free = 0.4051 target = 0.149277 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3379 r_free = 0.3379 target = 0.101154 restraints weight = 29971.738|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3335 r_free = 0.3335 target = 0.100340 restraints weight = 21780.400|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3338 r_free = 0.3338 target = 0.100291 restraints weight = 16826.124|
|-----------------------------------------------------------------------------|
r_work (final): 0.3312
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8070
moved from start:          0.2039

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  15238  Z= 0.169
  Angle     :  0.660  11.941  20820  Z= 0.318
  Chirality :  0.040   0.207   2599
  Planarity :  0.003   0.031   2529
  Dihedral  :  9.495 134.838   2956
  Min Nonbonded Distance : 2.425

Molprobity Statistics.
  All-atom Clashscore : 6.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.12 %
    Favored  : 97.88 %
  Rotamer:
    Outliers :  3.13 %
    Allowed  : 19.83 %
    Favored  : 77.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.25 (0.19), residues: 1935
  helix:  2.12 (0.14), residues: 1373
  sheet:  1.54 (0.49), residues: 107
  loop : -0.49 (0.29), residues: 455

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.060   0.002   TRP A1091 
 HIS   0.003   0.001   HIS B 502 
 PHE   0.031   0.001   PHE B 195 
 TYR   0.024   0.001   TYR B 309 
 ARG   0.002   0.000   ARG B 646 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04745 ( 1067)
  hydrogen bonds       : angle       3.70562 ( 3171)
  covalent geometry    : bond        0.00392 (15238)
  covalent geometry    : angle       0.66015 (20820)

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

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

  3870 Ramachandran restraints generated.
    1935 Oldfield, 0 Emsley, 1935 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3870 Ramachandran restraints generated.
    1935 Oldfield, 0 Emsley, 1935 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  223 residues out of total 1682 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 179
  time to evaluate  : 1.571 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  199 MET cc_start: 0.8547 (tpp) cc_final: 0.8266 (tpp)
REVERT: A  249 MET cc_start: 0.8413 (tmm) cc_final: 0.8043 (tmm)
REVERT: A  354 GLU cc_start: 0.7584 (OUTLIER) cc_final: 0.7163 (mp0)
REVERT: A  494 MET cc_start: 0.8707 (tpp) cc_final: 0.8206 (tpp)
REVERT: A  926 GLU cc_start: 0.8622 (mp0) cc_final: 0.7600 (mp0)
REVERT: B  187 ASN cc_start: 0.7485 (m-40) cc_final: 0.7195 (m-40)
REVERT: B  389 ILE cc_start: 0.9396 (OUTLIER) cc_final: 0.9163 (mp)
REVERT: B  494 MET cc_start: 0.8679 (tpp) cc_final: 0.8150 (tpp)
REVERT: B  848 GLU cc_start: 0.8269 (tp30) cc_final: 0.8008 (tp30)
  outliers start: 44
  outliers final: 33
  residues processed: 211
  average time/residue: 0.1936
  time to fit residues: 66.8863
Evaluate side-chains
  209 residues out of total 1682 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 174
  time to evaluate  : 1.534 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   79 VAL
Chi-restraints excluded: chain A residue   84 SER
Chi-restraints excluded: chain A residue  107 LEU
Chi-restraints excluded: chain A residue  184 LEU
Chi-restraints excluded: chain A residue  310 LEU
Chi-restraints excluded: chain A residue  354 GLU
Chi-restraints excluded: chain A residue  373 THR
Chi-restraints excluded: chain A residue  402 VAL
Chi-restraints excluded: chain A residue  464 VAL
Chi-restraints excluded: chain A residue  587 LEU
Chi-restraints excluded: chain A residue  844 ILE
Chi-restraints excluded: chain A residue  858 VAL
Chi-restraints excluded: chain A residue 1006 VAL
Chi-restraints excluded: chain A residue 1091 TRP
Chi-restraints excluded: chain A residue 1188 VAL
Chi-restraints excluded: chain B residue   78 ILE
Chi-restraints excluded: chain B residue   79 VAL
Chi-restraints excluded: chain B residue   84 SER
Chi-restraints excluded: chain B residue  107 LEU
Chi-restraints excluded: chain B residue  133 MET
Chi-restraints excluded: chain B residue  162 SER
Chi-restraints excluded: chain B residue  277 LEU
Chi-restraints excluded: chain B residue  310 LEU
Chi-restraints excluded: chain B residue  317 ILE
Chi-restraints excluded: chain B residue  319 LEU
Chi-restraints excluded: chain B residue  373 THR
Chi-restraints excluded: chain B residue  389 ILE
Chi-restraints excluded: chain B residue  390 ILE
Chi-restraints excluded: chain B residue  402 VAL
Chi-restraints excluded: chain B residue  464 VAL
Chi-restraints excluded: chain B residue  477 LEU
Chi-restraints excluded: chain B residue  587 LEU
Chi-restraints excluded: chain B residue  822 ILE
Chi-restraints excluded: chain B residue  844 ILE
Chi-restraints excluded: chain B residue  858 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 195
   random chunks:
   chunk 89 optimal weight:    5.9990
   chunk 188 optimal weight:   40.0000
   chunk 55 optimal weight:    8.9990
   chunk 133 optimal weight:    2.9990
   chunk 47 optimal weight:    6.9990
   chunk 50 optimal weight:    1.9990
   chunk 79 optimal weight:    8.9990
   chunk 147 optimal weight:    5.9990
   chunk 192 optimal weight:   40.0000
   chunk 116 optimal weight:    2.9990
   chunk 149 optimal weight:    0.0030
   overall best weight:    2.7998

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

Flipped N/Q/H residues before XYZ refinement:
** A 597 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 900 GLN
** B 597 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 900 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4038 r_free = 0.4038 target = 0.148237 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3402 r_free = 0.3402 target = 0.101835 restraints weight = 29460.430|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3342 r_free = 0.3342 target = 0.099545 restraints weight = 22969.745|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3357 r_free = 0.3357 target = 0.100482 restraints weight = 16916.356|
|-----------------------------------------------------------------------------|
r_work (final): 0.3341
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8037
moved from start:          0.2151

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  15238  Z= 0.183
  Angle     :  0.693  14.804  20820  Z= 0.333
  Chirality :  0.041   0.208   2599
  Planarity :  0.003   0.031   2529
  Dihedral  :  9.603 134.903   2956
  Min Nonbonded Distance : 2.388

Molprobity Statistics.
  All-atom Clashscore : 7.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.22 %
    Favored  : 97.78 %
  Rotamer:
    Outliers :  2.70 %
    Allowed  : 20.61 %
    Favored  : 76.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.19 (0.19), residues: 1935
  helix:  2.07 (0.14), residues: 1376
  sheet:  1.59 (0.49), residues: 105
  loop : -0.50 (0.29), residues: 454

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.059   0.002   TRP A1091 
 HIS   0.004   0.001   HIS B 981 
 PHE   0.014   0.001   PHE A 268 
 TYR   0.023   0.001   TYR B 309 
 ARG   0.004   0.000   ARG A 940 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04995 ( 1067)
  hydrogen bonds       : angle       3.78618 ( 3171)
  covalent geometry    : bond        0.00423 (15238)
  covalent geometry    : angle       0.69328 (20820)

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

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

  3870 Ramachandran restraints generated.
    1935 Oldfield, 0 Emsley, 1935 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3870 Ramachandran restraints generated.
    1935 Oldfield, 0 Emsley, 1935 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  214 residues out of total 1682 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 176
  time to evaluate  : 1.572 
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: A  249 MET cc_start: 0.8347 (tmm) cc_final: 0.7984 (tmm)
REVERT: A  354 GLU cc_start: 0.7725 (OUTLIER) cc_final: 0.7296 (mp0)
REVERT: A  494 MET cc_start: 0.8618 (tpp) cc_final: 0.8074 (tpp)
REVERT: A  926 GLU cc_start: 0.8583 (mp0) cc_final: 0.7576 (mp0)
REVERT: B  187 ASN cc_start: 0.7511 (m-40) cc_final: 0.7215 (m-40)
REVERT: B  388 LEU cc_start: 0.9552 (OUTLIER) cc_final: 0.9278 (tt)
REVERT: B  389 ILE cc_start: 0.9393 (OUTLIER) cc_final: 0.9121 (mp)
REVERT: B  494 MET cc_start: 0.8652 (tpp) cc_final: 0.8127 (tpp)
REVERT: B  823 LEU cc_start: 0.9235 (mt) cc_final: 0.8929 (pp)
  outliers start: 38
  outliers final: 31
  residues processed: 204
  average time/residue: 0.1957
  time to fit residues: 65.4164
Evaluate side-chains
  206 residues out of total 1682 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 172
  time to evaluate  : 1.518 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   79 VAL
Chi-restraints excluded: chain A residue   84 SER
Chi-restraints excluded: chain A residue  107 LEU
Chi-restraints excluded: chain A residue  184 LEU
Chi-restraints excluded: chain A residue  310 LEU
Chi-restraints excluded: chain A residue  354 GLU
Chi-restraints excluded: chain A residue  373 THR
Chi-restraints excluded: chain A residue  402 VAL
Chi-restraints excluded: chain A residue  464 VAL
Chi-restraints excluded: chain A residue  584 LEU
Chi-restraints excluded: chain A residue  587 LEU
Chi-restraints excluded: chain A residue  844 ILE
Chi-restraints excluded: chain A residue  858 VAL
Chi-restraints excluded: chain A residue 1006 VAL
Chi-restraints excluded: chain A residue 1188 VAL
Chi-restraints excluded: chain B residue   78 ILE
Chi-restraints excluded: chain B residue   79 VAL
Chi-restraints excluded: chain B residue   84 SER
Chi-restraints excluded: chain B residue  107 LEU
Chi-restraints excluded: chain B residue  133 MET
Chi-restraints excluded: chain B residue  162 SER
Chi-restraints excluded: chain B residue  277 LEU
Chi-restraints excluded: chain B residue  310 LEU
Chi-restraints excluded: chain B residue  319 LEU
Chi-restraints excluded: chain B residue  373 THR
Chi-restraints excluded: chain B residue  388 LEU
Chi-restraints excluded: chain B residue  389 ILE
Chi-restraints excluded: chain B residue  390 ILE
Chi-restraints excluded: chain B residue  402 VAL
Chi-restraints excluded: chain B residue  464 VAL
Chi-restraints excluded: chain B residue  477 LEU
Chi-restraints excluded: chain B residue  587 LEU
Chi-restraints excluded: chain B residue  822 ILE
Chi-restraints excluded: chain B residue  858 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 195
   random chunks:
   chunk 117 optimal weight:    0.7980
   chunk 81 optimal weight:    9.9990
   chunk 132 optimal weight:    5.9990
   chunk 68 optimal weight:    3.9990
   chunk 166 optimal weight:    3.9990
   chunk 171 optimal weight:    2.9990
   chunk 70 optimal weight:    0.8980
   chunk 193 optimal weight:    7.9990
   chunk 177 optimal weight:    9.9990
   chunk 94 optimal weight:   50.0000
   chunk 27 optimal weight:    0.1980
   overall best weight:    1.7784

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

Flipped N/Q/H residues before XYZ refinement:
** A 597 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 900 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 597 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 900 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4051 r_free = 0.4051 target = 0.148633 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3549 r_free = 0.3549 target = 0.110451 restraints weight = 29675.533|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3492 r_free = 0.3492 target = 0.108787 restraints weight = 41193.728|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3511 r_free = 0.3511 target = 0.110299 restraints weight = 23978.963|
|-----------------------------------------------------------------------------|
r_work (final): 0.3512
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7821
moved from start:          0.2140

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  15238  Z= 0.144
  Angle     :  0.685  13.782  20820  Z= 0.327
  Chirality :  0.040   0.218   2599
  Planarity :  0.003   0.032   2529
  Dihedral  :  9.441 134.900   2956
  Min Nonbonded Distance : 2.392

Molprobity Statistics.
  All-atom Clashscore : 7.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.91 %
    Favored  : 98.09 %
  Rotamer:
    Outliers :  2.70 %
    Allowed  : 20.90 %
    Favored  : 76.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.20 (0.19), residues: 1935
  helix:  2.06 (0.14), residues: 1379
  sheet:  1.54 (0.48), residues: 107
  loop : -0.45 (0.30), residues: 449

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.064   0.002   TRP B1091 
 HIS   0.002   0.001   HIS B 502 
 PHE   0.033   0.001   PHE A 195 
 TYR   0.024   0.001   TYR A1088 
 ARG   0.004   0.000   ARG A 573 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04766 ( 1067)
  hydrogen bonds       : angle       3.73041 ( 3171)
  covalent geometry    : bond        0.00322 (15238)
  covalent geometry    : angle       0.68471 (20820)

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

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

  3870 Ramachandran restraints generated.
    1935 Oldfield, 0 Emsley, 1935 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3870 Ramachandran restraints generated.
    1935 Oldfield, 0 Emsley, 1935 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  213 residues out of total 1682 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 175
  time to evaluate  : 1.643 
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: A  195 PHE cc_start: 0.7591 (t80) cc_final: 0.7094 (t80)
REVERT: A  249 MET cc_start: 0.8238 (tmm) cc_final: 0.7911 (tmm)
REVERT: A  277 LEU cc_start: 0.8979 (tp) cc_final: 0.8577 (mm)
REVERT: A  354 GLU cc_start: 0.7439 (OUTLIER) cc_final: 0.7064 (mp0)
REVERT: A  494 MET cc_start: 0.8516 (tpp) cc_final: 0.7983 (tpp)
REVERT: A  926 GLU cc_start: 0.8519 (mp0) cc_final: 0.7717 (mp0)
REVERT: B  187 ASN cc_start: 0.7604 (m-40) cc_final: 0.7346 (m-40)
REVERT: B  388 LEU cc_start: 0.9555 (OUTLIER) cc_final: 0.9281 (tt)
REVERT: B  389 ILE cc_start: 0.9282 (OUTLIER) cc_final: 0.9003 (mp)
REVERT: B  494 MET cc_start: 0.8534 (tpp) cc_final: 0.7994 (tpp)
REVERT: B  823 LEU cc_start: 0.9145 (mt) cc_final: 0.8902 (pp)
  outliers start: 38
  outliers final: 33
  residues processed: 204
  average time/residue: 0.1947
  time to fit residues: 65.2423
Evaluate side-chains
  206 residues out of total 1682 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 170
  time to evaluate  : 1.728 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   78 ILE
Chi-restraints excluded: chain A residue   79 VAL
Chi-restraints excluded: chain A residue   84 SER
Chi-restraints excluded: chain A residue  107 LEU
Chi-restraints excluded: chain A residue  184 LEU
Chi-restraints excluded: chain A residue  310 LEU
Chi-restraints excluded: chain A residue  354 GLU
Chi-restraints excluded: chain A residue  373 THR
Chi-restraints excluded: chain A residue  402 VAL
Chi-restraints excluded: chain A residue  464 VAL
Chi-restraints excluded: chain A residue  584 LEU
Chi-restraints excluded: chain A residue  587 LEU
Chi-restraints excluded: chain A residue  844 ILE
Chi-restraints excluded: chain A residue  858 VAL
Chi-restraints excluded: chain A residue 1006 VAL
Chi-restraints excluded: chain A residue 1188 VAL
Chi-restraints excluded: chain B residue   78 ILE
Chi-restraints excluded: chain B residue   79 VAL
Chi-restraints excluded: chain B residue   84 SER
Chi-restraints excluded: chain B residue  107 LEU
Chi-restraints excluded: chain B residue  133 MET
Chi-restraints excluded: chain B residue  162 SER
Chi-restraints excluded: chain B residue  277 LEU
Chi-restraints excluded: chain B residue  310 LEU
Chi-restraints excluded: chain B residue  317 ILE
Chi-restraints excluded: chain B residue  319 LEU
Chi-restraints excluded: chain B residue  373 THR
Chi-restraints excluded: chain B residue  388 LEU
Chi-restraints excluded: chain B residue  389 ILE
Chi-restraints excluded: chain B residue  390 ILE
Chi-restraints excluded: chain B residue  402 VAL
Chi-restraints excluded: chain B residue  464 VAL
Chi-restraints excluded: chain B residue  477 LEU
Chi-restraints excluded: chain B residue  587 LEU
Chi-restraints excluded: chain B residue  822 ILE
Chi-restraints excluded: chain B residue  858 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 195
   random chunks:
   chunk 161 optimal weight:    5.9990
   chunk 190 optimal weight:   30.0000
   chunk 178 optimal weight:   20.0000
   chunk 180 optimal weight:   50.0000
   chunk 79 optimal weight:    7.9990
   chunk 105 optimal weight:    7.9990
   chunk 38 optimal weight:    3.9990
   chunk 77 optimal weight:   30.0000
   chunk 51 optimal weight:   20.0000
   chunk 24 optimal weight:    0.2980
   chunk 150 optimal weight:    1.9990
   overall best weight:    4.0588

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

Flipped N/Q/H residues before XYZ refinement:
** A 597 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 900 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 458 HIS
** B 597 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 900 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4011 r_free = 0.4011 target = 0.145630 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3376 r_free = 0.3376 target = 0.100538 restraints weight = 29751.171|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3243 r_free = 0.3243 target = 0.094171 restraints weight = 24382.912|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3254 r_free = 0.3254 target = 0.095063 restraints weight = 22161.029|
|-----------------------------------------------------------------------------|
r_work (final): 0.3241
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8170
moved from start:          0.2379

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.052  15238  Z= 0.244
  Angle     :  0.761  13.204  20820  Z= 0.371
  Chirality :  0.043   0.282   2599
  Planarity :  0.003   0.033   2529
  Dihedral  :  9.941 135.097   2956
  Min Nonbonded Distance : 2.398

Molprobity Statistics.
  All-atom Clashscore : 8.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.64 %
    Favored  : 97.36 %
  Rotamer:
    Outliers :  2.99 %
    Allowed  : 20.47 %
    Favored  : 76.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.96 (0.19), residues: 1935
  helix:  1.85 (0.14), residues: 1382
  sheet:  1.66 (0.49), residues: 100
  loop : -0.45 (0.29), residues: 453

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.063   0.002   TRP B1091 
 HIS   0.003   0.001   HIS A 889 
 PHE   0.039   0.002   PHE A 195 
 TYR   0.025   0.001   TYR B 309 
 ARG   0.005   0.000   ARG A 573 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05756 ( 1067)
  hydrogen bonds       : angle       4.01440 ( 3171)
  covalent geometry    : bond        0.00568 (15238)
  covalent geometry    : angle       0.76117 (20820)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4208.94 seconds
wall clock time: 74 minutes 22.74 seconds (4462.74 seconds total)