Starting phenix.real_space_refine
on Sat Oct 11 12:17:45 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8u7s_41991/10_2025/8u7s_41991.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8u7s_41991/10_2025/8u7s_41991.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.18
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8u7s_41991/10_2025/8u7s_41991.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8u7s_41991/10_2025/8u7s_41991.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8u7s_41991/10_2025/8u7s_41991.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8u7s_41991/10_2025/8u7s_41991.cif"
  }
  resolution = 4.18
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.005
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       2      5.49       5
     S      74      5.16       5
     C    9562      2.51       5
     N    2366      2.21       5
     O    2626      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 3 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 14630
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 7134
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 908, 7134
          Classifications: {'peptide': 908}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 880}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 15
          Unresolved non-hydrogen angles: 19
          Unresolved non-hydrogen dihedrals: 11
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 8
    Chain: "B"
      Number of atoms: 7134
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 908, 7134
          Classifications: {'peptide': 908}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 880}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 15
          Unresolved non-hydrogen angles: 19
          Unresolved non-hydrogen dihedrals: 11
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 8
    Chain: "A"
      Number of atoms: 207
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 207
          Unusual residues: {'AJP': 2, 'POV': 2}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
          Unresolved non-hydrogen bonds: 71
          Unresolved non-hydrogen angles: 103
          Unresolved non-hydrogen dihedrals: 120
          Unresolved non-hydrogen chiralities: 19
    Chain: "B"
      Number of atoms: 155
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 155
          Unusual residues: {'AJP': 2, 'POV': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 72
          Unresolved non-hydrogen angles: 107
          Unresolved non-hydrogen dihedrals: 135
          Unresolved non-hydrogen chiralities: 24
  Time building chain proxies: 3.70, per 1000 atoms: 0.25
  Number of scatterers: 14630
  At special positions: 0
  Unit cell: (109.02, 120.06, 128.34, 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      74     16.00
     P       2     15.00
     O    2626      8.00
     N    2366      7.00
     C    9562      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: 1.55
  Conformation dependent library (CDL) restraints added in 449.0 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  3600 Ramachandran restraints generated.
    1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3412

  Finding SS restraints...
    Secondary structure from input PDB file:
      74 helices and 8 sheets defined
      74.4% alpha, 4.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.62
  Creating SS restraints...
    Processing helix  chain 'A' and resid 77 through 94
    Processing helix  chain 'A' and resid 102 through 120
    Processing helix  chain 'A' and resid 120 through 128
    Processing helix  chain 'A' and resid 134 through 151
      removed outlier: 3.646A  pdb=" N   LEU A 138 " --> pdb=" O   ASP A 134 " (cutoff:3.500A)
      removed outlier: 4.906A  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 162
      removed outlier: 3.811A  pdb=" N   SER A 162 " --> pdb=" O   THR A 158 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 162 through 189
    Processing helix  chain 'A' and resid 194 through 207
      removed outlier: 4.355A  pdb=" N   MET A 205 " --> pdb=" O   PHE A 201 " (cutoff:3.500A)
      removed outlier: 3.515A  pdb=" N   SER A 206 " --> pdb=" O   GLY A 202 " (cutoff:3.500A)
      removed outlier: 4.336A  pdb=" N   ALA A 207 " --> pdb=" O   ALA A 203 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 210 through 221
      removed outlier: 3.514A  pdb=" N   VAL A 214 " --> pdb=" O   PRO A 210 " (cutoff:3.500A)
      removed outlier: 5.474A  pdb=" N   ASP A 219 " --> pdb=" O   ALA A 215 " (cutoff:3.500A)
      removed outlier: 4.340A  pdb=" N   LEU A 220 " --> pdb=" O   LEU A 216 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 223 through 253
      removed outlier: 3.658A  pdb=" N   GLY A 227 " --> pdb=" O   SER A 223 " (cutoff:3.500A)
      removed outlier: 3.580A  pdb=" N   SER A 234 " --> pdb=" O   ILE A 230 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 260 through 291
      removed outlier: 4.295A  pdb=" N   LEU A 266 " --> pdb=" O   GLY A 262 " (cutoff:3.500A)
      removed outlier: 4.519A  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 298 through 319
      removed outlier: 3.724A  pdb=" N   THR A 302 " --> pdb=" O   LEU A 298 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 321 through 337
      removed outlier: 4.043A  pdb=" N   LEU A 325 " --> pdb=" O   VAL A 321 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 342 through 375
    Processing helix  chain 'A' and resid 376 through 380
      removed outlier: 3.506A  pdb=" N   ALA A 379 " --> pdb=" O   ALA A 376 " (cutoff:3.500A)
      removed outlier: 3.839A  pdb=" N   VAL A 380 " --> pdb=" O   LEU A 377 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 376 through 380'
    Processing helix  chain 'A' and resid 381 through 414
      removed outlier: 3.986A  pdb=" N   LEU A 388 " --> pdb=" O   ASP A 384 " (cutoff:3.500A)
      removed outlier: 4.634A  pdb=" N   ILE A 389 " --> pdb=" O   TRP A 385 " (cutoff:3.500A)
      removed outlier: 3.923A  pdb=" N   ILE A 390 " --> pdb=" O   PHE A 386 " (cutoff:3.500A)
      removed outlier: 3.679A  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
    Processing helix  chain 'A' and resid 432 through 447
      removed outlier: 3.917A  pdb=" N   LEU A 436 " --> pdb=" O   GLY A 432 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 449 through 481
      removed outlier: 3.956A  pdb=" N   SER A 453 " --> pdb=" O   ASP A 449 " (cutoff:3.500A)
      removed outlier: 4.185A  pdb=" N   VAL A 468 " --> pdb=" O   VAL A 464 " (cutoff:3.500A)
      removed outlier: 4.476A  pdb=" N   ALA A 471 " --> pdb=" O   LEU A 467 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 487 through 514
      removed outlier: 3.797A  pdb=" N   SER A 514 " --> pdb=" O   ASN A 510 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 522 through 530
      removed outlier: 3.767A  pdb=" N   CYS A 530 " --> pdb=" O   ALA A 526 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 572 through 601
      removed outlier: 3.600A  pdb=" N   GLY A 601 " --> pdb=" O   GLN A 597 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 604 through 621
      removed outlier: 3.713A  pdb=" N   GLU A 621 " --> pdb=" O   VAL A 617 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 627 through 636
      removed outlier: 3.765A  pdb=" N   LEU A 631 " --> pdb=" O   LEU A 627 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 637 through 639
      No H-bonds generated for 'chain 'A' and resid 637 through 639'
    Processing helix  chain 'A' and resid 640 through 653
      removed outlier: 3.978A  pdb=" N   LEU A 644 " --> pdb=" O   ILE A 640 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 813 through 854
      removed outlier: 3.682A  pdb=" N   LEU A 817 " --> pdb=" O   LEU A 813 " (cutoff:3.500A)
      Proline residue:  A 819  - end of helix
      removed outlier: 3.639A  pdb=" N   ASN A 831 " --> pdb=" O   GLY A 827 " (cutoff:3.500A)
      removed outlier: 5.073A  pdb=" N   GLN A 832 " --> pdb=" O   LYS A 828 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 855 through 857
      No H-bonds generated for 'chain 'A' and resid 855 through 857'
    Processing helix  chain 'A' and resid 860 through 889
      removed outlier: 3.505A  pdb=" N   HIS A 889 " --> pdb=" O   LEU A 885 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 889 through 919
      removed outlier: 4.055A  pdb=" N   ALA A 893 " --> pdb=" O   HIS A 889 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 923 through 943
      removed outlier: 3.597A  pdb=" N   ASN A 943 " --> pdb=" O   LYS A 939 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 952 through 959
    Processing helix  chain 'A' and resid 960 through 964
      removed outlier: 3.791A  pdb=" N   LEU A 963 " --> pdb=" O   VAL A 960 " (cutoff:3.500A)
      removed outlier: 3.865A  pdb=" N   ALA A 964 " --> pdb=" O   SER A 961 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 960 through 964'
    Processing helix  chain 'A' and resid 966 through 977
      removed outlier: 3.782A  pdb=" N   ILE A 970 " --> pdb=" O   ASP A 966 " (cutoff:3.500A)
      removed outlier: 4.094A  pdb=" N   ARG A 976 " --> pdb=" O   PHE A 972 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1044 through 1049
      removed outlier: 3.816A  pdb=" N   LEU A1048 " --> pdb=" O   GLU A1044 " (cutoff:3.500A)
      removed outlier: 3.580A  pdb=" N   THR A1049 " --> pdb=" O   MET A1045 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 1044 through 1049'
    Processing helix  chain 'A' and resid 1070 through 1080
    Processing helix  chain 'A' and resid 1085 through 1107
      Proline residue:  A1101  - end of helix
      removed outlier: 3.930A  pdb=" N   GLN A1106 " --> pdb=" O   LEU A1102 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1113 through 1123
    Processing helix  chain 'B' and resid 77 through 94
    Processing helix  chain 'B' and resid 102 through 120
    Processing helix  chain 'B' and resid 120 through 128
    Processing helix  chain 'B' and resid 134 through 151
      removed outlier: 3.631A  pdb=" N   LEU B 138 " --> pdb=" O   ASP B 134 " (cutoff:3.500A)
      removed outlier: 4.857A  pdb=" N   LEU B 143 " --> pdb=" O   LEU B 139 " (cutoff:3.500A)
      Proline residue:  B 144  - end of helix
      removed outlier: 3.688A  pdb=" N   SER B 150 " --> pdb=" O   LEU B 146 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   ALA B 151 " --> pdb=" O   ILE B 147 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 155 through 162
      removed outlier: 3.866A  pdb=" N   SER B 162 " --> pdb=" O   THR B 158 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 162 through 189
      removed outlier: 3.508A  pdb=" N   VAL B 166 " --> pdb=" O   SER B 162 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   PHE B 189 " --> pdb=" O   ALA B 185 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 194 through 207
      removed outlier: 4.219A  pdb=" N   MET B 205 " --> pdb=" O   PHE B 201 " (cutoff:3.500A)
      removed outlier: 3.537A  pdb=" N   SER B 206 " --> pdb=" O   GLY B 202 " (cutoff:3.500A)
      removed outlier: 4.410A  pdb=" N   ALA B 207 " --> pdb=" O   ALA B 203 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 210 through 221
      removed outlier: 5.216A  pdb=" N   ASP B 219 " --> pdb=" O   ALA B 215 " (cutoff:3.500A)
      removed outlier: 4.200A  pdb=" N   LEU B 220 " --> pdb=" O   LEU B 216 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 223 through 253
      removed outlier: 3.814A  pdb=" N   GLY B 227 " --> pdb=" O   SER B 223 " (cutoff:3.500A)
      removed outlier: 3.587A  pdb=" N   SER B 234 " --> pdb=" O   ILE B 230 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 260 through 291
      removed outlier: 3.539A  pdb=" N   ASN B 264 " --> pdb=" O   THR B 260 " (cutoff:3.500A)
      removed outlier: 4.268A  pdb=" N   LEU B 266 " --> pdb=" O   GLY B 262 " (cutoff:3.500A)
      removed outlier: 4.534A  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 298 through 319
      removed outlier: 3.733A  pdb=" N   THR B 302 " --> pdb=" O   LEU B 298 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 321 through 337
      removed outlier: 4.066A  pdb=" N   LEU B 325 " --> pdb=" O   VAL B 321 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 342 through 375
    Processing helix  chain 'B' and resid 376 through 380
      removed outlier: 3.526A  pdb=" N   ALA B 379 " --> pdb=" O   ALA B 376 " (cutoff:3.500A)
      removed outlier: 3.788A  pdb=" N   VAL B 380 " --> pdb=" O   LEU B 377 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 376 through 380'
    Processing helix  chain 'B' and resid 381 through 414
      removed outlier: 3.870A  pdb=" N   LEU B 388 " --> pdb=" O   ASP B 384 " (cutoff:3.500A)
      removed outlier: 4.601A  pdb=" N   ILE B 389 " --> pdb=" O   TRP B 385 " (cutoff:3.500A)
      removed outlier: 3.963A  pdb=" N   ILE B 390 " --> pdb=" O   PHE B 386 " (cutoff:3.500A)
      removed outlier: 3.612A  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
    Processing helix  chain 'B' and resid 432 through 447
      removed outlier: 3.908A  pdb=" N   LEU B 436 " --> pdb=" O   GLY B 432 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 449 through 481
      removed outlier: 3.966A  pdb=" N   SER B 453 " --> pdb=" O   ASP B 449 " (cutoff:3.500A)
      removed outlier: 4.206A  pdb=" N   VAL B 468 " --> pdb=" O   VAL B 464 " (cutoff:3.500A)
      removed outlier: 4.446A  pdb=" N   ALA B 471 " --> pdb=" O   LEU B 467 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 482 through 485
      removed outlier: 3.602A  pdb=" N   ASP B 485 " --> pdb=" O   GLY B 482 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 482 through 485'
    Processing helix  chain 'B' and resid 487 through 514
      removed outlier: 3.752A  pdb=" N   SER B 514 " --> pdb=" O   ASN B 510 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 522 through 530
      removed outlier: 3.525A  pdb=" N   ALA B 526 " --> pdb=" O   ASP B 522 " (cutoff:3.500A)
      removed outlier: 3.714A  pdb=" N   CYS B 530 " --> pdb=" O   ALA B 526 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 572 through 601
      removed outlier: 3.576A  pdb=" N   GLY B 601 " --> pdb=" O   GLN B 597 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 604 through 621
      removed outlier: 3.710A  pdb=" N   GLU B 621 " --> pdb=" O   VAL B 617 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 627 through 636
      removed outlier: 3.737A  pdb=" N   LEU B 631 " --> pdb=" O   LEU B 627 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 637 through 640
    Processing helix  chain 'B' and resid 641 through 653
    Processing helix  chain 'B' and resid 813 through 854
      removed outlier: 3.586A  pdb=" N   LEU B 817 " --> pdb=" O   LEU B 813 " (cutoff:3.500A)
      Proline residue:  B 819  - end of helix
      removed outlier: 4.309A  pdb=" N   GLN B 832 " --> pdb=" O   LYS B 828 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 860 through 889
      removed outlier: 3.509A  pdb=" N   HIS B 889 " --> pdb=" O   LEU B 885 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 889 through 919
      removed outlier: 4.054A  pdb=" N   ALA B 893 " --> pdb=" O   HIS B 889 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 923 through 943
      removed outlier: 3.596A  pdb=" N   ASN B 943 " --> pdb=" O   LYS B 939 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 952 through 959
    Processing helix  chain 'B' and resid 960 through 964
      removed outlier: 3.733A  pdb=" N   LEU B 963 " --> pdb=" O   VAL B 960 " (cutoff:3.500A)
      removed outlier: 3.820A  pdb=" N   ALA B 964 " --> pdb=" O   SER B 961 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 960 through 964'
    Processing helix  chain 'B' and resid 966 through 977
      removed outlier: 3.583A  pdb=" N   ILE B 970 " --> pdb=" O   ASP B 966 " (cutoff:3.500A)
      removed outlier: 4.094A  pdb=" N   ARG B 976 " --> pdb=" O   PHE B 972 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1044 through 1049
      removed outlier: 3.739A  pdb=" N   LEU B1048 " --> pdb=" O   GLU B1044 " (cutoff:3.500A)
      removed outlier: 3.614A  pdb=" N   THR B1049 " --> pdb=" O   MET B1045 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 1044 through 1049'
    Processing helix  chain 'B' and resid 1070 through 1080
    Processing helix  chain 'B' and resid 1085 through 1107
      Proline residue:  B1101  - end of helix
      removed outlier: 3.928A  pdb=" N   GLN B1106 " --> pdb=" O   LEU B1102 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1113 through 1123
    Processing sheet with id=AA1, first strand: chain 'A' and resid 978 through 982
      removed outlier: 6.489A  pdb=" N   GLN A1064 " --> pdb=" O   VAL A1002 " (cutoff:3.500A)
      removed outlier: 3.651A  pdb=" N   PHE A 999 " --> pdb=" O   ILE A1042 " (cutoff:3.500A)
      removed outlier: 3.688A  pdb=" N   ILE A1042 " --> pdb=" O   PHE A 999 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 1033 through 1035
    Processing sheet with id=AA3, first strand: chain 'A' and resid 1125 through 1127
      removed outlier: 3.807A  pdb=" N   TYR A1125 " --> pdb=" O   VAL A1188 " (cutoff:3.500A)
      removed outlier: 4.091A  pdb=" N   VAL A1188 " --> pdb=" O   TYR A1125 " (cutoff:3.500A)
      removed outlier: 3.769A  pdb=" N   VAL A1127 " --> pdb=" O   LEU A1186 " (cutoff:3.500A)
      removed outlier: 4.790A  pdb=" N   LEU A1186 " --> pdb=" O   VAL A1127 " (cutoff:3.500A)
      removed outlier: 6.792A  pdb=" N   ARG A1185 " --> pdb=" O   ILE A1148 " (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 978 through 982
      removed outlier: 6.502A  pdb=" N   GLN B1064 " --> pdb=" O   VAL B1002 " (cutoff:3.500A)
      removed outlier: 3.593A  pdb=" N   PHE B 999 " --> pdb=" O   ILE B1042 " (cutoff:3.500A)
      removed outlier: 3.661A  pdb=" N   ILE B1042 " --> pdb=" O   PHE B 999 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 1033 through 1035
    Processing sheet with id=AA7, first strand: chain 'B' and resid 1126 through 1127
      removed outlier: 3.765A  pdb=" N   VAL B1127 " --> pdb=" O   LEU B1186 " (cutoff:3.500A)
      removed outlier: 4.782A  pdb=" N   LEU B1186 " --> pdb=" O   VAL B1127 " (cutoff:3.500A)
      removed outlier: 6.772A  pdb=" N   ARG B1185 " --> pdb=" O   ILE B1148 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 1135 through 1137

    989 hydrogen bonds defined for protein.
    2940 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: 2.45

  Time building geometry restraints manager: 1.92 seconds

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

  Histogram of bond lengths:
        1.20 -     1.33: 2553
        1.33 -     1.45: 3587
        1.45 -     1.57: 8655
        1.57 -     1.69: 3
        1.69 -     1.82: 136
  Bond restraints: 14934
  Sorted by residual:
  bond pdb=" O12 POV A1401 "
       pdb=" P   POV A1401 "
    ideal  model  delta    sigma   weight residual
    1.657  1.495  0.162 2.00e-02 2.50e+03 6.55e+01
  bond pdb=" C   ILE B 818 "
       pdb=" N   PRO B 819 "
    ideal  model  delta    sigma   weight residual
    1.335  1.365 -0.030 1.28e-02 6.10e+03 5.63e+00
  bond pdb=" N   PRO B 951 "
       pdb=" CD  PRO B 951 "
    ideal  model  delta    sigma   weight residual
    1.473  1.451  0.022 1.40e-02 5.10e+03 2.43e+00
  bond pdb=" C   TYR A 641 "
       pdb=" N   PRO A 642 "
    ideal  model  delta    sigma   weight residual
    1.334  1.370 -0.036 2.34e-02 1.83e+03 2.39e+00
  bond pdb=" C26 AJP B1403 "
       pdb=" O25 AJP B1403 "
    ideal  model  delta    sigma   weight residual
    1.375  1.405 -0.030 2.00e-02 2.50e+03 2.30e+00
  ... (remaining 14929 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.72: 20011
        2.72 -     5.44: 241
        5.44 -     8.16: 37
        8.16 -    10.88: 7
       10.88 -    13.59: 1
  Bond angle restraints: 20297
  Sorted by residual:
  angle pdb=" O11 POV A1401 "
        pdb=" P   POV A1401 "
        pdb=" O12 POV A1401 "
      ideal   model   delta    sigma   weight residual
      97.67  111.26  -13.59 3.00e+00 1.11e-01 2.05e+01
  angle pdb=" C   LYS B 622 "
        pdb=" N   ASP B 623 "
        pdb=" CA  ASP B 623 "
      ideal   model   delta    sigma   weight residual
     121.54  128.65   -7.11 1.91e+00 2.74e-01 1.39e+01
  angle pdb=" C   LYS A 622 "
        pdb=" N   ASP A 623 "
        pdb=" CA  ASP A 623 "
      ideal   model   delta    sigma   weight residual
     121.54  128.58   -7.04 1.91e+00 2.74e-01 1.36e+01
  angle pdb=" N   ILE A 829 "
        pdb=" CA  ILE A 829 "
        pdb=" C   ILE A 829 "
      ideal   model   delta    sigma   weight residual
     112.96  109.37    3.59 1.00e+00 1.00e+00 1.29e+01
  angle pdb=" CB  MET A 160 "
        pdb=" CG  MET A 160 "
        pdb=" SD  MET A 160 "
      ideal   model   delta    sigma   weight residual
     112.70  122.76  -10.06 3.00e+00 1.11e-01 1.12e+01
  ... (remaining 20292 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    25.67: 8825
       25.67 -    51.34: 512
       51.34 -    77.01: 70
       77.01 -   102.68: 11
      102.68 -   128.35: 18
  Dihedral angle restraints: 9436
    sinusoidal: 4166
      harmonic: 5270
  Sorted by residual:
  dihedral pdb=" C55 AJP A1403 "
           pdb=" C59 AJP A1403 "
           pdb=" O60 AJP A1403 "
           pdb=" C58 AJP A1403 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.14   68.21 -128.35     1      3.00e+01 1.11e-03 1.73e+01
  dihedral pdb=" C59 AJP B1403 "
           pdb=" C55 AJP B1403 "
           pdb=" O60 AJP B1403 "
           pdb=" O54 AJP B1403 "
      ideal   model   delta sinusoidal    sigma   weight residual
     177.58   61.18  116.40     1      3.00e+01 1.11e-03 1.54e+01
  dihedral pdb=" C59 AJP A1404 "
           pdb=" C55 AJP A1404 "
           pdb=" O60 AJP A1404 "
           pdb=" O54 AJP A1404 "
      ideal   model   delta sinusoidal    sigma   weight residual
     177.58   61.18  116.40     1      3.00e+01 1.11e-03 1.54e+01
  ... (remaining 9433 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.041: 1733
       0.041 -    0.083: 548
       0.083 -    0.124: 164
       0.124 -    0.165: 21
       0.165 -    0.206: 14
  Chirality restraints: 2480
  Sorted by residual:
  chirality pdb=" C10 AJP A1403 "
            pdb=" C08 AJP A1403 "
            pdb=" C11 AJP A1403 "
            pdb=" O82 AJP A1403 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.61    2.40    0.21 2.00e-01 2.50e+01 1.07e+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    2.40    0.20 2.00e-01 2.50e+01 1.03e+00
  chirality pdb=" C10 AJP A1404 "
            pdb=" C08 AJP A1404 "
            pdb=" C11 AJP A1404 "
            pdb=" O82 AJP A1404 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.61    2.41    0.20 2.00e-01 2.50e+01 9.97e-01
  ... (remaining 2477 not shown)

  Planarity restraints: 2449
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP B 635 "    0.023 2.00e-02 2.50e+03   2.39e-02 1.43e+01
        pdb=" CG  TRP B 635 "   -0.064 2.00e-02 2.50e+03
        pdb=" CD1 TRP B 635 "    0.031 2.00e-02 2.50e+03
        pdb=" CD2 TRP B 635 "    0.000 2.00e-02 2.50e+03
        pdb=" NE1 TRP B 635 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE2 TRP B 635 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE3 TRP B 635 "    0.008 2.00e-02 2.50e+03
        pdb=" CZ2 TRP B 635 "   -0.000 2.00e-02 2.50e+03
        pdb=" CZ3 TRP B 635 "    0.003 2.00e-02 2.50e+03
        pdb=" CH2 TRP B 635 "    0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR B1083 "   -0.046 5.00e-02 4.00e+02   7.09e-02 8.04e+00
        pdb=" N   PRO B1084 "    0.123 5.00e-02 4.00e+02
        pdb=" CA  PRO B1084 "   -0.036 5.00e-02 4.00e+02
        pdb=" CD  PRO B1084 "   -0.040 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR A1083 "    0.046 5.00e-02 4.00e+02   7.07e-02 7.99e+00
        pdb=" N   PRO A1084 "   -0.122 5.00e-02 4.00e+02
        pdb=" CA  PRO A1084 "    0.036 5.00e-02 4.00e+02
        pdb=" CD  PRO A1084 "    0.040 5.00e-02 4.00e+02
  ... (remaining 2446 not shown)

  Histogram of nonbonded interaction distances:
        2.25 -     2.78: 3074
        2.78 -     3.31: 14485
        3.31 -     3.84: 23453
        3.84 -     4.37: 23728
        4.37 -     4.90: 42935
  Nonbonded interactions: 107675
  Sorted by model distance:
  nonbonded pdb=" OG1 THR B1179 "
            pdb=" O   GLU B1182 "
     model   vdw
     2.255 3.040
  nonbonded pdb=" OG1 THR A1179 "
            pdb=" O   GLU A1182 "
     model   vdw
     2.255 3.040
  nonbonded pdb=" NZ  LYS A 897 "
            pdb=" OD2 ASP B 520 "
     model   vdw
     2.289 3.120
  nonbonded pdb=" OD2 ASP A 520 "
            pdb=" NZ  LYS B 897 "
     model   vdw
     2.311 3.120
  nonbonded pdb=" NZ  LYS A 937 "
            pdb=" O   GLU B 531 "
     model   vdw
     2.318 3.120
  ... (remaining 107670 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 1192 or (resid 1401 and (name C1 or name C2 or  \ 
name C21 or name C22 or name C23 or name C24 or name C25 or name C26 or name C27 \ 
 or name C28 or name C29 or name C3 or name C31 or name C32 or name C33 or name  \ 
C34 or name C35 or name C36 or name C37 or name C38 or name C39 or name O11 or n \ 
ame O21 or name O22 or name O31 or name O32 or name C210 or name C211 or name C2 \ 
12 or name C213 or name C214 or name C215 or name C216 or name C310 or name C311 \ 
 or name C312 or name C313 or name C314)) or resid 1403))
  selection = (chain 'B' and (resid 76 through 1401 or (resid 1403 and (name C01 or name C02 o \ 
r name C03 or name C04 or name C05 or name C06 or name C07 or name C08 or name C \ 
10 or name C11 or name C12 or name C13 or name C14 or name C15 or name C16 or na \ 
me C17 or name C18 or name C19 or name C20 or name C21 or name C22 or name C23 o \ 
r name C24 or name C26 or name C27 or name C28 or name C29 or name C30 or name C \ 
32 or name C35 or name C36 or name C37 or name C38 or name C39 or name C41 or na \ 
me C55 or name C56 or name C57 or name C58 or name C59 or name C80 or name C81 o \ 
r name C83 or name C85 or name O09 or name O25 or name O31 or name O33 or name O \ 
34 or name O40 or name O42 or name O43 or name O44 or name O54 or name O60 or na \ 
me O63 or name O64 or name O76 or name O77 or name O78 or name O79 or name O82 o \ 
r name O84))))
}

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:             0.320
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.140
  Check model and map are aligned:         0.020
  Set scattering table:                    0.050
  Process input model:                     14.680
  Find NCS groups from input model:        0.270
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:1.330
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.850
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8021
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      :  0.004   0.162  14934  Z= 0.195
  Angle     :  0.746  13.594  20297  Z= 0.365
  Chirality :  0.046   0.206   2480
  Planarity :  0.005   0.071   2449
  Dihedral  : 16.685 128.348   6024
  Min Nonbonded Distance : 2.255

Molprobity Statistics.
  All-atom Clashscore : 6.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.33 %
    Favored  : 97.67 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.26 %
    Favored  : 99.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.97 (0.20), residues: 1800
  helix:  1.36 (0.14), residues: 1236
  sheet:  0.08 (0.51), residues: 100
  loop : -1.09 (0.28), residues: 464

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B1162 
 TYR   0.017   0.001   TYR B 309 
 PHE   0.041   0.002   PHE A 195 
 TRP   0.064   0.002   TRP B 635 
 HIS   0.003   0.001   HIS B 350 

Details of bonding type rmsd
  covalent geometry    : bond        0.00406 (14934)
  covalent geometry    : angle       0.74574 (20297)
  hydrogen bonds       : bond        0.12653 (  989)
  hydrogen bonds       : angle       5.10878 ( 2940)

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

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

  3600 Ramachandran restraints generated.
    1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3600 Ramachandran restraints generated.
    1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  225 residues out of total 1556 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 225
  time to evaluate  : 0.555 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  160 MET cc_start: 0.7879 (mmm) cc_final: 0.7592 (ttp)
REVERT: A  578 MET cc_start: 0.8078 (ppp) cc_final: 0.7863 (ppp)
REVERT: A  971 ASP cc_start: 0.7380 (p0) cc_final: 0.6940 (p0)
REVERT: B  160 MET cc_start: 0.7829 (mmm) cc_final: 0.7617 (ttp)
REVERT: B  643 TRP cc_start: 0.4990 (t-100) cc_final: 0.4468 (t-100)
  outliers start: 0
  outliers final: 0
  residues processed: 225
  average time/residue: 0.1001
  time to fit residues: 35.7173
Evaluate side-chains
  165 residues out of total 1556 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 165
  time to evaluate  : 0.607 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 180
   random chunks:
   chunk 98 optimal weight:    5.9990
   chunk 107 optimal weight:    0.9980
   chunk 10 optimal weight:    0.7980
   chunk 66 optimal weight:    2.9990
   chunk 130 optimal weight:   10.0000
   chunk 124 optimal weight:    4.9990
   chunk 103 optimal weight:    1.9990
   chunk 77 optimal weight:    9.9990
   chunk 122 optimal weight:    6.9990
   chunk 91 optimal weight:    1.9990
   chunk 149 optimal weight:    4.9990
   overall best weight:    1.7586

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

Flipped N/Q/H residues before XYZ refinement:
A 889 HIS
B1074 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3763 r_free = 0.3763 target = 0.145825 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3423 r_free = 0.3423 target = 0.118899 restraints weight = 23783.347|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3383 r_free = 0.3383 target = 0.116611 restraints weight = 23903.825|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3392 r_free = 0.3392 target = 0.117426 restraints weight = 30556.751|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3405 r_free = 0.3405 target = 0.118447 restraints weight = 22376.246|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3409 r_free = 0.3409 target = 0.118852 restraints weight = 19436.534|
|-----------------------------------------------------------------------------|
r_work (final): 0.3411
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8079
moved from start:          0.0888

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  14934  Z= 0.149
  Angle     :  0.586   6.576  20297  Z= 0.292
  Chirality :  0.039   0.150   2480
  Planarity :  0.004   0.073   2449
  Dihedral  :  9.409  86.656   2692
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 5.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.94 %
    Favored  : 98.06 %
  Rotamer:
    Outliers :  0.06 %
    Allowed  :  5.43 %
    Favored  : 94.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.72 (0.20), residues: 1800
  helix:  2.00 (0.14), residues: 1248
  sheet:  0.01 (0.54), residues: 92
  loop : -1.05 (0.28), residues: 460

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 161 
 TYR   0.019   0.001   TYR B 309 
 PHE   0.026   0.001   PHE B 195 
 TRP   0.039   0.002   TRP B 635 
 HIS   0.004   0.001   HIS A 350 

Details of bonding type rmsd
  covalent geometry    : bond        0.00330 (14934)
  covalent geometry    : angle       0.58566 (20297)
  hydrogen bonds       : bond        0.05388 (  989)
  hydrogen bonds       : angle       3.99444 ( 2940)

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

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

  3600 Ramachandran restraints generated.
    1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3600 Ramachandran restraints generated.
    1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  216 residues out of total 1556 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 215
  time to evaluate  : 0.456 
Fit side-chains
   revert: symmetry clash
REVERT: A  578 MET cc_start: 0.8159 (ppp) cc_final: 0.7909 (ppp)
REVERT: A  854 ILE cc_start: 0.9095 (tp) cc_final: 0.8857 (tp)
REVERT: B  643 TRP cc_start: 0.5110 (t-100) cc_final: 0.4508 (t-100)
REVERT: B  848 GLU cc_start: 0.7777 (tt0) cc_final: 0.7360 (tt0)
REVERT: B 1107 MET cc_start: 0.8023 (ttt) cc_final: 0.7797 (ttm)
  outliers start: 1
  outliers final: 0
  residues processed: 216
  average time/residue: 0.1009
  time to fit residues: 34.7843
Evaluate side-chains
  152 residues out of total 1556 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 152
  time to evaluate  : 0.509 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 180
   random chunks:
   chunk 73 optimal weight:    9.9990
   chunk 61 optimal weight:    6.9990
   chunk 40 optimal weight:   10.0000
   chunk 36 optimal weight:    0.6980
   chunk 165 optimal weight:    0.2980
   chunk 168 optimal weight:    2.9990
   chunk 10 optimal weight:    0.9990
   chunk 95 optimal weight:    0.9980
   chunk 79 optimal weight:    8.9990
   chunk 65 optimal weight:    9.9990
   chunk 16 optimal weight:    0.8980
   overall best weight:    0.7782

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

Flipped N/Q/H residues before XYZ refinement:
A 889 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3795 r_free = 0.3795 target = 0.148527 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.121166 restraints weight = 23821.020|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3431 r_free = 0.3431 target = 0.119837 restraints weight = 23456.128|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3445 r_free = 0.3445 target = 0.121025 restraints weight = 22995.396|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3450 r_free = 0.3450 target = 0.121455 restraints weight = 19042.581|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3452 r_free = 0.3452 target = 0.121702 restraints weight = 18843.553|
|-----------------------------------------------------------------------------|
r_work (final): 0.3462
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8029
moved from start:          0.1162

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026  14934  Z= 0.113
  Angle     :  0.536   7.213  20297  Z= 0.265
  Chirality :  0.038   0.146   2480
  Planarity :  0.004   0.073   2449
  Dihedral  :  8.214  79.418   2692
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 4.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.83 %
    Favored  : 98.17 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.81 %
    Favored  : 96.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.07 (0.20), residues: 1800
  helix:  2.30 (0.14), residues: 1246
  sheet:  0.26 (0.55), residues: 92
  loop : -1.04 (0.28), residues: 462

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 161 
 TYR   0.015   0.001   TYR B 309 
 PHE   0.020   0.001   PHE B 195 
 TRP   0.040   0.001   TRP A 635 
 HIS   0.003   0.001   HIS A 350 

Details of bonding type rmsd
  covalent geometry    : bond        0.00226 (14934)
  covalent geometry    : angle       0.53561 (20297)
  hydrogen bonds       : bond        0.04609 (  989)
  hydrogen bonds       : angle       3.71507 ( 2940)

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

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

  3600 Ramachandran restraints generated.
    1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3600 Ramachandran restraints generated.
    1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  216 residues out of total 1556 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 216
  time to evaluate  : 0.552 
Fit side-chains
REVERT: A   97 LYS cc_start: 0.8112 (mmmt) cc_final: 0.7878 (pttp)
REVERT: A  295 ASN cc_start: 0.8280 (t0) cc_final: 0.8055 (t0)
REVERT: A  578 MET cc_start: 0.7897 (ppp) cc_final: 0.7544 (ppp)
REVERT: A  882 LEU cc_start: 0.9185 (tp) cc_final: 0.8913 (tp)
REVERT: B  199 MET cc_start: 0.8820 (mpp) cc_final: 0.8545 (mpp)
REVERT: B  643 TRP cc_start: 0.4916 (t-100) cc_final: 0.4501 (t-100)
REVERT: B  848 GLU cc_start: 0.7762 (tt0) cc_final: 0.7482 (tt0)
REVERT: B 1107 MET cc_start: 0.7746 (ttt) cc_final: 0.7525 (ttm)
  outliers start: 0
  outliers final: 0
  residues processed: 216
  average time/residue: 0.1012
  time to fit residues: 34.9530
Evaluate side-chains
  151 residues out of total 1556 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 151
  time to evaluate  : 0.567 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 180
   random chunks:
   chunk 23 optimal weight:    1.9990
   chunk 166 optimal weight:    8.9990
   chunk 106 optimal weight:    1.9990
   chunk 153 optimal weight:    6.9990
   chunk 154 optimal weight:    0.8980
   chunk 104 optimal weight:    4.9990
   chunk 134 optimal weight:    4.9990
   chunk 84 optimal weight:    0.4980
   chunk 127 optimal weight:    0.7980
   chunk 175 optimal weight:    0.7980
   chunk 78 optimal weight:    3.9990
   overall best weight:    0.9982

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

Flipped N/Q/H residues before XYZ refinement:
A 889 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3794 r_free = 0.3794 target = 0.148576 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3447 r_free = 0.3447 target = 0.120574 restraints weight = 23901.629|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.120753 restraints weight = 26086.781|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3459 r_free = 0.3459 target = 0.122132 restraints weight = 24634.969|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3463 r_free = 0.3463 target = 0.122518 restraints weight = 19769.721|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3466 r_free = 0.3466 target = 0.122850 restraints weight = 19690.240|
|-----------------------------------------------------------------------------|
r_work (final): 0.3470
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7998
moved from start:          0.1340

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029  14934  Z= 0.115
  Angle     :  0.542   7.447  20297  Z= 0.265
  Chirality :  0.038   0.143   2480
  Planarity :  0.004   0.077   2449
  Dihedral  :  7.433  79.797   2692
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 4.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.72 %
    Favored  : 98.28 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.75 %
    Favored  : 96.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.28 (0.20), residues: 1800
  helix:  2.44 (0.14), residues: 1246
  sheet:  0.34 (0.56), residues: 92
  loop : -0.90 (0.29), residues: 462

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 420 
 TYR   0.016   0.001   TYR B 309 
 PHE   0.018   0.001   PHE A 195 
 TRP   0.045   0.002   TRP B 635 
 HIS   0.002   0.000   HIS A 350 

Details of bonding type rmsd
  covalent geometry    : bond        0.00244 (14934)
  covalent geometry    : angle       0.54231 (20297)
  hydrogen bonds       : bond        0.04438 (  989)
  hydrogen bonds       : angle       3.62567 ( 2940)

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

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

  3600 Ramachandran restraints generated.
    1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3600 Ramachandran restraints generated.
    1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  212 residues out of total 1556 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 212
  time to evaluate  : 0.556 
Fit side-chains
   revert: symmetry clash
REVERT: A  295 ASN cc_start: 0.8219 (t0) cc_final: 0.7956 (t0)
REVERT: A  578 MET cc_start: 0.7954 (ppp) cc_final: 0.7626 (ppp)
REVERT: A  848 GLU cc_start: 0.7658 (tt0) cc_final: 0.7242 (tt0)
REVERT: A  857 MET cc_start: 0.7229 (mmp) cc_final: 0.6986 (tpt)
REVERT: A  882 LEU cc_start: 0.9085 (tp) cc_final: 0.8874 (tp)
REVERT: B  186 MET cc_start: 0.6901 (mmt) cc_final: 0.6657 (mmt)
REVERT: B  295 ASN cc_start: 0.8279 (t0) cc_final: 0.8038 (t0)
REVERT: B  643 TRP cc_start: 0.4980 (t-100) cc_final: 0.4561 (t-100)
REVERT: B  848 GLU cc_start: 0.7767 (tt0) cc_final: 0.7425 (tt0)
  outliers start: 0
  outliers final: 0
  residues processed: 212
  average time/residue: 0.0976
  time to fit residues: 33.0949
Evaluate side-chains
  151 residues out of total 1556 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 151
  time to evaluate  : 0.554 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 180
   random chunks:
   chunk 29 optimal weight:    0.7980
   chunk 36 optimal weight:    1.9990
   chunk 106 optimal weight:    0.9980
   chunk 33 optimal weight:    6.9990
   chunk 17 optimal weight:    0.6980
   chunk 76 optimal weight:    6.9990
   chunk 158 optimal weight:    0.4980
   chunk 120 optimal weight:    3.9990
   chunk 118 optimal weight:    0.8980
   chunk 35 optimal weight:    5.9990
   chunk 68 optimal weight:   10.0000
   overall best weight:    0.7780

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3807 r_free = 0.3807 target = 0.149656 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 66)----------------|
| r_work = 0.3470 r_free = 0.3470 target = 0.122218 restraints weight = 23657.570|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3455 r_free = 0.3455 target = 0.121529 restraints weight = 26949.755|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3472 r_free = 0.3472 target = 0.122944 restraints weight = 26758.260|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3475 r_free = 0.3475 target = 0.123277 restraints weight = 19589.444|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.123887 restraints weight = 19604.437|
|-----------------------------------------------------------------------------|
r_work (final): 0.3487
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7978
moved from start:          0.1453

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028  14934  Z= 0.110
  Angle     :  0.532   7.256  20297  Z= 0.261
  Chirality :  0.038   0.140   2480
  Planarity :  0.004   0.076   2449
  Dihedral  :  7.229  76.853   2692
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 5.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.61 %
    Favored  : 98.39 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.78 %
    Favored  : 97.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.38 (0.20), residues: 1800
  helix:  2.49 (0.14), residues: 1244
  sheet:  0.43 (0.56), residues: 92
  loop : -0.79 (0.29), residues: 464

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 646 
 TYR   0.015   0.001   TYR B 309 
 PHE   0.031   0.001   PHE B 365 
 TRP   0.047   0.002   TRP B 635 
 HIS   0.002   0.000   HIS A 350 

Details of bonding type rmsd
  covalent geometry    : bond        0.00229 (14934)
  covalent geometry    : angle       0.53157 (20297)
  hydrogen bonds       : bond        0.04267 (  989)
  hydrogen bonds       : angle       3.57695 ( 2940)

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

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

  3600 Ramachandran restraints generated.
    1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3600 Ramachandran restraints generated.
    1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  217 residues out of total 1556 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 217
  time to evaluate  : 0.564 
Fit side-chains
REVERT: A  578 MET cc_start: 0.7811 (ppp) cc_final: 0.7585 (ppp)
REVERT: A  848 GLU cc_start: 0.7769 (tt0) cc_final: 0.7372 (tt0)
REVERT: A  857 MET cc_start: 0.7256 (mmp) cc_final: 0.7036 (tpt)
REVERT: A  882 LEU cc_start: 0.9120 (tp) cc_final: 0.8887 (tp)
REVERT: B  199 MET cc_start: 0.8585 (mpp) cc_final: 0.8157 (mpp)
REVERT: B  295 ASN cc_start: 0.8207 (t0) cc_final: 0.7972 (t0)
REVERT: B  578 MET cc_start: 0.7618 (ppp) cc_final: 0.7213 (ppp)
REVERT: B  643 TRP cc_start: 0.4890 (t-100) cc_final: 0.4512 (t-100)
REVERT: B  848 GLU cc_start: 0.7707 (tt0) cc_final: 0.7374 (tt0)
  outliers start: 0
  outliers final: 0
  residues processed: 217
  average time/residue: 0.1035
  time to fit residues: 35.8707
Evaluate side-chains
  155 residues out of total 1556 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 155
  time to evaluate  : 0.514 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 180
   random chunks:
   chunk 91 optimal weight:    0.7980
   chunk 134 optimal weight:    0.9990
   chunk 106 optimal weight:    4.9990
   chunk 67 optimal weight:    5.9990
   chunk 114 optimal weight:    5.9990
   chunk 50 optimal weight:    6.9990
   chunk 117 optimal weight:    1.9990
   chunk 108 optimal weight:    7.9990
   chunk 121 optimal weight:    3.9990
   chunk 36 optimal weight:    0.5980
   chunk 175 optimal weight:    8.9990
   overall best weight:    1.6786

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3773 r_free = 0.3773 target = 0.146986 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3431 r_free = 0.3431 target = 0.119785 restraints weight = 23713.332|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3401 r_free = 0.3401 target = 0.117949 restraints weight = 24905.639|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3415 r_free = 0.3415 target = 0.119141 restraints weight = 24699.437|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3419 r_free = 0.3419 target = 0.119499 restraints weight = 20270.796|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3421 r_free = 0.3421 target = 0.119730 restraints weight = 20279.489|
|-----------------------------------------------------------------------------|
r_work (final): 0.3426
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8072
moved from start:          0.1554

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  14934  Z= 0.140
  Angle     :  0.563   6.682  20297  Z= 0.281
  Chirality :  0.039   0.147   2480
  Planarity :  0.004   0.077   2449
  Dihedral  :  7.237  76.754   2692
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 5.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.06 %
    Favored  : 97.94 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.04 %
    Favored  : 96.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.25 (0.20), residues: 1800
  helix:  2.39 (0.14), residues: 1248
  sheet:  0.36 (0.56), residues: 92
  loop : -0.84 (0.29), residues: 460

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 583 
 TYR   0.019   0.001   TYR B 309 
 PHE   0.040   0.001   PHE B 195 
 TRP   0.049   0.002   TRP B 635 
 HIS   0.002   0.001   HIS A 350 

Details of bonding type rmsd
  covalent geometry    : bond        0.00319 (14934)
  covalent geometry    : angle       0.56318 (20297)
  hydrogen bonds       : bond        0.04720 (  989)
  hydrogen bonds       : angle       3.68165 ( 2940)

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

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

  3600 Ramachandran restraints generated.
    1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3600 Ramachandran restraints generated.
    1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  212 residues out of total 1556 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 212
  time to evaluate  : 0.564 
Fit side-chains
REVERT: A  178 SER cc_start: 0.9387 (m) cc_final: 0.8689 (t)
REVERT: A  295 ASN cc_start: 0.8285 (t0) cc_final: 0.8062 (t0)
REVERT: A  848 GLU cc_start: 0.7744 (tt0) cc_final: 0.7389 (tt0)
REVERT: A  857 MET cc_start: 0.7385 (mmp) cc_final: 0.7122 (tpt)
REVERT: A  882 LEU cc_start: 0.9116 (tp) cc_final: 0.8847 (tp)
REVERT: B  295 ASN cc_start: 0.8190 (t0) cc_final: 0.7941 (t0)
REVERT: B  578 MET cc_start: 0.7707 (ppp) cc_final: 0.7382 (ppp)
REVERT: B  643 TRP cc_start: 0.5155 (t-100) cc_final: 0.4660 (t-100)
REVERT: B  848 GLU cc_start: 0.7639 (tt0) cc_final: 0.7303 (tt0)
  outliers start: 0
  outliers final: 0
  residues processed: 212
  average time/residue: 0.0989
  time to fit residues: 34.0518
Evaluate side-chains
  154 residues out of total 1556 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 154
  time to evaluate  : 0.503 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 180
   random chunks:
   chunk 179 optimal weight:    8.9990
   chunk 127 optimal weight:    8.9990
   chunk 134 optimal weight:    1.9990
   chunk 117 optimal weight:    0.9990
   chunk 94 optimal weight:    0.7980
   chunk 43 optimal weight:    0.9990
   chunk 2 optimal weight:    0.6980
   chunk 97 optimal weight:    0.9980
   chunk 162 optimal weight:   20.0000
   chunk 149 optimal weight:    7.9990
   chunk 45 optimal weight:    3.9990
   overall best weight:    0.8984

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3810 r_free = 0.3810 target = 0.149957 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3464 r_free = 0.3464 target = 0.121955 restraints weight = 23456.100|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3450 r_free = 0.3450 target = 0.121260 restraints weight = 25218.323|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3465 r_free = 0.3465 target = 0.122611 restraints weight = 25202.737|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3469 r_free = 0.3469 target = 0.122971 restraints weight = 19909.474|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3471 r_free = 0.3471 target = 0.123182 restraints weight = 20761.414|
|-----------------------------------------------------------------------------|
r_work (final): 0.3460
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8008
moved from start:          0.1617

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029  14934  Z= 0.114
  Angle     :  0.542   6.873  20297  Z= 0.269
  Chirality :  0.038   0.152   2480
  Planarity :  0.004   0.077   2449
  Dihedral  :  7.034  73.195   2692
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 5.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.61 %
    Favored  : 98.39 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.68 %
    Favored  : 98.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.33 (0.20), residues: 1800
  helix:  2.48 (0.14), residues: 1236
  sheet:  0.37 (0.55), residues: 92
  loop : -0.82 (0.29), residues: 472

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 646 
 TYR   0.015   0.001   TYR A 309 
 PHE   0.043   0.001   PHE B 195 
 TRP   0.049   0.002   TRP A 635 
 HIS   0.002   0.001   HIS B 350 

Details of bonding type rmsd
  covalent geometry    : bond        0.00241 (14934)
  covalent geometry    : angle       0.54208 (20297)
  hydrogen bonds       : bond        0.04345 (  989)
  hydrogen bonds       : angle       3.59318 ( 2940)

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

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

  3600 Ramachandran restraints generated.
    1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3600 Ramachandran restraints generated.
    1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  224 residues out of total 1556 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 224
  time to evaluate  : 0.499 
Fit side-chains
REVERT: A  178 SER cc_start: 0.9412 (m) cc_final: 0.8636 (t)
REVERT: A  848 GLU cc_start: 0.7789 (tt0) cc_final: 0.7440 (tt0)
REVERT: A  882 LEU cc_start: 0.9210 (tp) cc_final: 0.8932 (tp)
REVERT: B  349 LEU cc_start: 0.9304 (mm) cc_final: 0.9079 (mt)
REVERT: B  578 MET cc_start: 0.7644 (ppp) cc_final: 0.7229 (ppp)
REVERT: B  643 TRP cc_start: 0.5205 (t-100) cc_final: 0.4737 (t-100)
REVERT: B  848 GLU cc_start: 0.7664 (tt0) cc_final: 0.7304 (tt0)
  outliers start: 0
  outliers final: 0
  residues processed: 224
  average time/residue: 0.1002
  time to fit residues: 36.3311
Evaluate side-chains
  160 residues out of total 1556 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 160
  time to evaluate  : 0.569 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 180
   random chunks:
   chunk 60 optimal weight:    8.9990
   chunk 106 optimal weight:    0.6980
   chunk 30 optimal weight:    5.9990
   chunk 155 optimal weight:    6.9990
   chunk 126 optimal weight:    0.9990
   chunk 0 optimal weight:    5.9990
   chunk 28 optimal weight:    2.9990
   chunk 109 optimal weight:    4.9990
   chunk 91 optimal weight:    0.9980
   chunk 27 optimal weight:    0.7980
   chunk 47 optimal weight:    2.9990
   overall best weight:    1.2984

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3783 r_free = 0.3783 target = 0.147710 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3430 r_free = 0.3430 target = 0.119433 restraints weight = 23726.938|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3418 r_free = 0.3418 target = 0.119153 restraints weight = 25526.193|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3432 r_free = 0.3432 target = 0.120388 restraints weight = 25113.669|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3439 r_free = 0.3439 target = 0.120950 restraints weight = 18297.549|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.121249 restraints weight = 17036.253|
|-----------------------------------------------------------------------------|
r_work (final): 0.3450
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8026
moved from start:          0.1676

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  14934  Z= 0.126
  Angle     :  0.568   7.134  20297  Z= 0.280
  Chirality :  0.038   0.176   2480
  Planarity :  0.004   0.077   2449
  Dihedral  :  7.086  74.025   2692
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 5.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.83 %
    Favored  : 98.17 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.36 %
    Favored  : 98.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.32 (0.20), residues: 1800
  helix:  2.44 (0.15), residues: 1246
  sheet:  0.32 (0.55), residues: 92
  loop : -0.77 (0.29), residues: 462

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 856 
 TYR   0.019   0.001   TYR A 309 
 PHE   0.062   0.001   PHE A 195 
 TRP   0.054   0.002   TRP B 635 
 HIS   0.002   0.001   HIS A 350 

Details of bonding type rmsd
  covalent geometry    : bond        0.00280 (14934)
  covalent geometry    : angle       0.56827 (20297)
  hydrogen bonds       : bond        0.04490 (  989)
  hydrogen bonds       : angle       3.63776 ( 2940)

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

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

  3600 Ramachandran restraints generated.
    1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3600 Ramachandran restraints generated.
    1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  212 residues out of total 1556 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 212
  time to evaluate  : 0.592 
Fit side-chains
REVERT: A  178 SER cc_start: 0.9403 (m) cc_final: 0.8789 (t)
REVERT: A  199 MET cc_start: 0.8472 (mpp) cc_final: 0.8260 (mpp)
REVERT: A  295 ASN cc_start: 0.8154 (t0) cc_final: 0.7924 (t0)
REVERT: A  848 GLU cc_start: 0.7792 (tt0) cc_final: 0.7462 (tt0)
REVERT: A  882 LEU cc_start: 0.9186 (tp) cc_final: 0.8892 (tp)
REVERT: B  154 MET cc_start: 0.7560 (mmm) cc_final: 0.7152 (tpt)
REVERT: B  295 ASN cc_start: 0.8089 (t0) cc_final: 0.7864 (t0)
REVERT: B  578 MET cc_start: 0.7612 (ppp) cc_final: 0.7272 (ppp)
REVERT: B  643 TRP cc_start: 0.5184 (t-100) cc_final: 0.4699 (t-100)
REVERT: B  848 GLU cc_start: 0.7697 (tt0) cc_final: 0.7361 (tt0)
  outliers start: 0
  outliers final: 0
  residues processed: 212
  average time/residue: 0.0984
  time to fit residues: 33.7877
Evaluate side-chains
  156 residues out of total 1556 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 156
  time to evaluate  : 0.507 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 180
   random chunks:
   chunk 150 optimal weight:    9.9990
   chunk 104 optimal weight:    6.9990
   chunk 153 optimal weight:    1.9990
   chunk 154 optimal weight:    2.9990
   chunk 85 optimal weight:    2.9990
   chunk 34 optimal weight:    0.9980
   chunk 5 optimal weight:    0.0670
   chunk 33 optimal weight:    6.9990
   chunk 71 optimal weight:    9.9990
   chunk 60 optimal weight:    5.9990
   chunk 68 optimal weight:    0.5980
   overall best weight:    1.3322

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3782 r_free = 0.3782 target = 0.147693 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3439 r_free = 0.3439 target = 0.120098 restraints weight = 23600.904|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3431 r_free = 0.3431 target = 0.119854 restraints weight = 24966.187|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3437 r_free = 0.3437 target = 0.120442 restraints weight = 26366.380|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3448 r_free = 0.3448 target = 0.121339 restraints weight = 21038.740|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3452 r_free = 0.3452 target = 0.121769 restraints weight = 18984.430|
|-----------------------------------------------------------------------------|
r_work (final): 0.3456
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8026
moved from start:          0.1693

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  14934  Z= 0.128
  Angle     :  0.566   7.148  20297  Z= 0.282
  Chirality :  0.039   0.154   2480
  Planarity :  0.004   0.077   2449
  Dihedral  :  7.144  74.879   2692
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 5.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.83 %
    Favored  : 98.17 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.84 %
    Favored  : 99.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.29 (0.20), residues: 1800
  helix:  2.41 (0.14), residues: 1246
  sheet:  0.25 (0.54), residues: 92
  loop : -0.75 (0.29), residues: 462

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 646 
 TYR   0.021   0.001   TYR B 309 
 PHE   0.042   0.001   PHE A 195 
 TRP   0.063   0.002   TRP B 635 
 HIS   0.002   0.001   HIS A 350 

Details of bonding type rmsd
  covalent geometry    : bond        0.00285 (14934)
  covalent geometry    : angle       0.56640 (20297)
  hydrogen bonds       : bond        0.04536 (  989)
  hydrogen bonds       : angle       3.66773 ( 2940)

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

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

  3600 Ramachandran restraints generated.
    1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3600 Ramachandran restraints generated.
    1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  211 residues out of total 1556 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 211
  time to evaluate  : 0.651 
Fit side-chains
   revert: symmetry clash
REVERT: A  178 SER cc_start: 0.9335 (m) cc_final: 0.8640 (t)
REVERT: A  848 GLU cc_start: 0.7759 (tt0) cc_final: 0.7412 (tt0)
REVERT: A  882 LEU cc_start: 0.9216 (tp) cc_final: 0.8901 (tp)
REVERT: B  154 MET cc_start: 0.7731 (mmm) cc_final: 0.7114 (tpt)
REVERT: B  578 MET cc_start: 0.7623 (ppp) cc_final: 0.7223 (ppp)
REVERT: B  643 TRP cc_start: 0.5136 (t-100) cc_final: 0.4651 (t-100)
REVERT: B  848 GLU cc_start: 0.7672 (tt0) cc_final: 0.7313 (tt0)
  outliers start: 0
  outliers final: 0
  residues processed: 211
  average time/residue: 0.1005
  time to fit residues: 34.3053
Evaluate side-chains
  155 residues out of total 1556 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 155
  time to evaluate  : 0.578 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 180
   random chunks:
   chunk 81 optimal weight:    0.9990
   chunk 16 optimal weight:    0.9980
   chunk 149 optimal weight:    0.5980
   chunk 143 optimal weight:    0.0370
   chunk 17 optimal weight:    4.9990
   chunk 0 optimal weight:    4.9990
   chunk 10 optimal weight:    0.7980
   chunk 30 optimal weight:   10.0000
   chunk 52 optimal weight:    6.9990
   chunk 110 optimal weight:    2.9990
   chunk 132 optimal weight:    3.9990
   overall best weight:    0.6860

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

Flipped N/Q/H residues before XYZ refinement:
B 270 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3803 r_free = 0.3803 target = 0.149421 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3457 r_free = 0.3457 target = 0.121428 restraints weight = 23679.182|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3439 r_free = 0.3439 target = 0.120537 restraints weight = 27267.263|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.121883 restraints weight = 26922.206|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3461 r_free = 0.3461 target = 0.122457 restraints weight = 20282.506|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3463 r_free = 0.3463 target = 0.122711 restraints weight = 19263.972|
|-----------------------------------------------------------------------------|
r_work (final): 0.3474
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8012
moved from start:          0.1822

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035  14934  Z= 0.112
  Angle     :  0.557   7.446  20297  Z= 0.274
  Chirality :  0.038   0.165   2480
  Planarity :  0.004   0.078   2449
  Dihedral  :  6.850  75.177   2692
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 5.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.44 %
    Favored  : 98.56 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.39 %
    Favored  : 99.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.37 (0.20), residues: 1800
  helix:  2.47 (0.15), residues: 1246
  sheet:  0.29 (0.54), residues: 92
  loop : -0.74 (0.29), residues: 462

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 585 
 TYR   0.015   0.001   TYR B 309 
 PHE   0.039   0.001   PHE B 195 
 TRP   0.058   0.002   TRP B 635 
 HIS   0.002   0.000   HIS B 350 

Details of bonding type rmsd
  covalent geometry    : bond        0.00237 (14934)
  covalent geometry    : angle       0.55687 (20297)
  hydrogen bonds       : bond        0.04157 (  989)
  hydrogen bonds       : angle       3.60978 ( 2940)

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

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

  3600 Ramachandran restraints generated.
    1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3600 Ramachandran restraints generated.
    1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  220 residues out of total 1556 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 220
  time to evaluate  : 0.571 
Fit side-chains
REVERT: A  178 SER cc_start: 0.9324 (m) cc_final: 0.8597 (t)
REVERT: A  848 GLU cc_start: 0.7687 (tt0) cc_final: 0.7372 (tt0)
REVERT: B  154 MET cc_start: 0.7742 (mmm) cc_final: 0.7171 (tpt)
REVERT: B  160 MET cc_start: 0.7902 (mmm) cc_final: 0.7640 (ttp)
REVERT: B  511 MET cc_start: 0.8758 (tmm) cc_final: 0.8553 (tmm)
REVERT: B  578 MET cc_start: 0.7632 (ppp) cc_final: 0.7260 (ppp)
REVERT: B  643 TRP cc_start: 0.5083 (t-100) cc_final: 0.4647 (t-100)
REVERT: B  848 GLU cc_start: 0.7581 (tt0) cc_final: 0.7258 (tt0)
  outliers start: 0
  outliers final: 0
  residues processed: 220
  average time/residue: 0.0957
  time to fit residues: 34.0595
Evaluate side-chains
  158 residues out of total 1556 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 158
  time to evaluate  : 0.557 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 180
   random chunks:
   chunk 44 optimal weight:    3.9990
   chunk 139 optimal weight:    1.9990
   chunk 145 optimal weight:    0.0570
   chunk 78 optimal weight:    3.9990
   chunk 5 optimal weight:    3.9990
   chunk 110 optimal weight:    5.9990
   chunk 34 optimal weight:    4.9990
   chunk 166 optimal weight:    8.9990
   chunk 127 optimal weight:    4.9990
   chunk 74 optimal weight:    3.9990
   chunk 27 optimal weight:    2.9990
   overall best weight:    2.6106

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

Flipped N/Q/H residues before XYZ refinement:
B 889 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3741 r_free = 0.3741 target = 0.144294 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.116931 restraints weight = 23768.164|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3384 r_free = 0.3384 target = 0.116321 restraints weight = 29121.573|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.117542 restraints weight = 27786.211|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3401 r_free = 0.3401 target = 0.117754 restraints weight = 20746.891|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3404 r_free = 0.3404 target = 0.117992 restraints weight = 22630.941|
|-----------------------------------------------------------------------------|
r_work (final): 0.3405
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8084
moved from start:          0.1862

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044  14934  Z= 0.187
  Angle     :  0.631   7.305  20297  Z= 0.317
  Chirality :  0.041   0.152   2480
  Planarity :  0.004   0.078   2449
  Dihedral  :  7.151  77.385   2692
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 6.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.33 %
    Favored  : 97.67 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.52 %
    Favored  : 99.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.12 (0.20), residues: 1800
  helix:  2.29 (0.14), residues: 1242
  sheet:  0.17 (0.55), residues: 92
  loop : -0.82 (0.29), residues: 466

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  92 
 TYR   0.024   0.001   TYR B 309 
 PHE   0.039   0.002   PHE B 195 
 TRP   0.048   0.002   TRP B 635 
 HIS   0.003   0.001   HIS B 350 

Details of bonding type rmsd
  covalent geometry    : bond        0.00437 (14934)
  covalent geometry    : angle       0.63107 (20297)
  hydrogen bonds       : bond        0.05321 (  989)
  hydrogen bonds       : angle       3.84591 ( 2940)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1857.18 seconds
wall clock time: 33 minutes 8.15 seconds (1988.15 seconds total)