Starting phenix.real_space_refine
on Wed Jul 30 07:07:10 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7xjy_33237/07_2025/7xjy_33237.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7xjy_33237/07_2025/7xjy_33237.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7xjy_33237/07_2025/7xjy_33237.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7xjy_33237/07_2025/7xjy_33237.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7xjy_33237/07_2025/7xjy_33237.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7xjy_33237/07_2025/7xjy_33237.cif"
  }
  resolution = 3.6
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.001 sd=   0.133
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      48      5.16       5
     C    7713      2.51       5
     N    2061      2.21       5
     O    2248      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 32 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 12070
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 6034
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 763, 6034
          Classifications: {'peptide': 763}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PCIS': 3, 'PTRANS': 32, 'TRANS': 727}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 15
          Unresolved non-hydrogen angles: 17
          Unresolved non-hydrogen dihedrals: 13
          Planarities with less than four sites: {'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 10
    Chain: "B"
      Number of atoms: 6036
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 763, 6036
          Classifications: {'peptide': 763}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PCIS': 3, 'PTRANS': 32, 'TRANS': 727}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 13
          Unresolved non-hydrogen angles: 15
          Unresolved non-hydrogen dihedrals: 11
          Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 9
  Time building chain proxies: 8.64, per 1000 atoms: 0.72
  Number of scatterers: 12070
  At special positions: 0
  Unit cell: (150.7, 122.1, 86.9, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      48     16.00
     O    2248      8.00
     N    2061      7.00
     C    7713      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: 3.29
  Conformation dependent library (CDL) restraints added in 1.7 seconds
  

  3028 Ramachandran restraints generated.
    1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2856

  Finding SS restraints...
    Secondary structure from input PDB file:
      65 helices and 16 sheets defined
      54.4% alpha, 19.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 2.19
  Creating SS restraints...
    Processing helix  chain 'A' and resid 31 through 47
      removed outlier: 3.834A  pdb=" N   ALA A  35 " --> pdb=" O   THR A  31 " (cutoff:3.500A)
      removed outlier: 3.816A  pdb=" N   GLY A  47 " --> pdb=" O   TRP A  43 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 60 through 64
    Processing helix  chain 'A' and resid 88 through 91
      removed outlier: 3.545A  pdb=" N   SER A  91 " --> pdb=" O   PRO A  88 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 88 through 91'
    Processing helix  chain 'A' and resid 116 through 128
    Processing helix  chain 'A' and resid 190 through 199
      removed outlier: 3.502A  pdb=" N   GLY A 199 " --> pdb=" O   MET A 195 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 202 through 205
      removed outlier: 3.512A  pdb=" N   ASN A 205 " --> pdb=" O   HIS A 202 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 202 through 205'
    Processing helix  chain 'A' and resid 214 through 231
      removed outlier: 5.540A  pdb=" N   GLU A 220 " --> pdb=" O   GLU A 216 " (cutoff:3.500A)
      removed outlier: 5.167A  pdb=" N   ASN A 221 " --> pdb=" O   LEU A 217 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 235 through 255
      removed outlier: 3.638A  pdb=" N   LEU A 255 " --> pdb=" O   SER A 251 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 257 through 278
      removed outlier: 3.912A  pdb=" N   ALA A 261 " --> pdb=" O   LEU A 257 " (cutoff:3.500A)
      removed outlier: 3.826A  pdb=" N   ARG A 278 " --> pdb=" O   ILE A 274 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 284 through 311
      removed outlier: 4.071A  pdb=" N   ARG A 288 " --> pdb=" O   THR A 284 " (cutoff:3.500A)
      removed outlier: 3.519A  pdb=" N   LEU A 311 " --> pdb=" O   THR A 307 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 354 through 376
    Processing helix  chain 'A' and resid 466 through 480
      Proline residue:  A 474  - end of helix
      removed outlier: 3.601A  pdb=" N   ILE A 480 " --> pdb=" O   ILE A 476 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 538 through 540
      No H-bonds generated for 'chain 'A' and resid 538 through 540'
    Processing helix  chain 'A' and resid 541 through 549
    Processing helix  chain 'A' and resid 556 through 572
    Processing helix  chain 'A' and resid 580 through 591
      removed outlier: 3.723A  pdb=" N   VAL A 591 " --> pdb=" O   VAL A 587 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 602 through 608
      removed outlier: 3.778A  pdb=" N   PHE A 605 " --> pdb=" O   ASP A 602 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 609 through 620
      removed outlier: 3.685A  pdb=" N   LEU A 613 " --> pdb=" O   PRO A 609 " (cutoff:3.500A)
      removed outlier: 3.952A  pdb=" N   HIS A 620 " --> pdb=" O   VAL A 616 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 647 through 673
      removed outlier: 3.591A  pdb=" N   VAL A 651 " --> pdb=" O   LYS A 647 " (cutoff:3.500A)
      removed outlier: 4.083A  pdb=" N   LYS A 671 " --> pdb=" O   LYS A 667 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 677 through 682
      removed outlier: 4.003A  pdb=" N   PHE A 681 " --> pdb=" O   LYS A 677 " (cutoff:3.500A)
      removed outlier: 3.857A  pdb=" N   ARG A 682 " --> pdb=" O   LEU A 678 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 677 through 682'
    Processing helix  chain 'A' and resid 683 through 687
      removed outlier: 3.828A  pdb=" N   SER A 686 " --> pdb=" O   ASP A 683 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 697 through 706
    Processing helix  chain 'A' and resid 707 through 715
    Processing helix  chain 'A' and resid 718 through 720
      No H-bonds generated for 'chain 'A' and resid 718 through 720'
    Processing helix  chain 'A' and resid 721 through 730
    Processing helix  chain 'A' and resid 738 through 744
    Processing helix  chain 'A' and resid 745 through 748
      removed outlier: 3.588A  pdb=" N   ALA A 748 " --> pdb=" O   THR A 745 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 745 through 748'
    Processing helix  chain 'A' and resid 749 through 760
    Processing helix  chain 'A' and resid 762 through 772
    Processing helix  chain 'A' and resid 785 through 807
    Processing helix  chain 'A' and resid 818 through 833
      removed outlier: 3.558A  pdb=" N   ILE A 822 " --> pdb=" O   GLY A 818 " (cutoff:3.500A)
      removed outlier: 3.551A  pdb=" N   SER A 823 " --> pdb=" O   LEU A 819 " (cutoff:3.500A)
      removed outlier: 4.636A  pdb=" N   TYR A 824 " --> pdb=" O   ARG A 820 " (cutoff:3.500A)
      removed outlier: 3.928A  pdb=" N   VAL A 827 " --> pdb=" O   SER A 823 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 838 through 850
      removed outlier: 3.503A  pdb=" N   GLU A 849 " --> pdb=" O   LEU A 845 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 855 through 874
    Processing helix  chain 'B' and resid 31 through 47
      removed outlier: 3.856A  pdb=" N   ALA B  35 " --> pdb=" O   THR B  31 " (cutoff:3.500A)
      removed outlier: 3.822A  pdb=" N   GLY B  47 " --> pdb=" O   TRP B  43 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 60 through 64
    Processing helix  chain 'B' and resid 88 through 91
      removed outlier: 3.551A  pdb=" N   SER B  91 " --> pdb=" O   PRO B  88 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 88 through 91'
    Processing helix  chain 'B' and resid 116 through 128
    Processing helix  chain 'B' and resid 190 through 199
    Processing helix  chain 'B' and resid 202 through 205
      removed outlier: 3.507A  pdb=" N   ASN B 205 " --> pdb=" O   HIS B 202 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 202 through 205'
    Processing helix  chain 'B' and resid 214 through 231
      removed outlier: 5.743A  pdb=" N   GLU B 220 " --> pdb=" O   GLU B 216 " (cutoff:3.500A)
      removed outlier: 5.111A  pdb=" N   ASN B 221 " --> pdb=" O   LEU B 217 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 235 through 255
      removed outlier: 3.696A  pdb=" N   LEU B 255 " --> pdb=" O   SER B 251 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 257 through 278
      removed outlier: 3.899A  pdb=" N   ALA B 261 " --> pdb=" O   LEU B 257 " (cutoff:3.500A)
      removed outlier: 3.840A  pdb=" N   ARG B 278 " --> pdb=" O   ILE B 274 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 284 through 311
      removed outlier: 4.093A  pdb=" N   ARG B 288 " --> pdb=" O   THR B 284 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 354 through 376
    Processing helix  chain 'B' and resid 466 through 480
      Proline residue:  B 474  - end of helix
      removed outlier: 3.641A  pdb=" N   ILE B 480 " --> pdb=" O   ILE B 476 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 538 through 540
      No H-bonds generated for 'chain 'B' and resid 538 through 540'
    Processing helix  chain 'B' and resid 541 through 549
      removed outlier: 3.504A  pdb=" N   ALA B 549 " --> pdb=" O   THR B 545 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 556 through 572
    Processing helix  chain 'B' and resid 580 through 591
      removed outlier: 3.747A  pdb=" N   VAL B 591 " --> pdb=" O   VAL B 587 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 602 through 608
      removed outlier: 3.787A  pdb=" N   PHE B 605 " --> pdb=" O   ASP B 602 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 609 through 620
      removed outlier: 3.697A  pdb=" N   LEU B 613 " --> pdb=" O   PRO B 609 " (cutoff:3.500A)
      removed outlier: 3.957A  pdb=" N   HIS B 620 " --> pdb=" O   VAL B 616 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 647 through 674
      removed outlier: 3.595A  pdb=" N   VAL B 651 " --> pdb=" O   LYS B 647 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 679 through 687
      removed outlier: 3.829A  pdb=" N   SER B 686 " --> pdb=" O   ASP B 683 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 697 through 706
    Processing helix  chain 'B' and resid 707 through 715
    Processing helix  chain 'B' and resid 718 through 720
      No H-bonds generated for 'chain 'B' and resid 718 through 720'
    Processing helix  chain 'B' and resid 721 through 730
    Processing helix  chain 'B' and resid 738 through 744
    Processing helix  chain 'B' and resid 745 through 748
      removed outlier: 3.526A  pdb=" N   ALA B 748 " --> pdb=" O   THR B 745 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 745 through 748'
    Processing helix  chain 'B' and resid 749 through 760
    Processing helix  chain 'B' and resid 762 through 772
    Processing helix  chain 'B' and resid 785 through 807
    Processing helix  chain 'B' and resid 819 through 833
    Processing helix  chain 'B' and resid 838 through 850
    Processing helix  chain 'B' and resid 855 through 874
    Processing sheet with id=AA1, first strand: chain 'A' and resid 49 through 50
      removed outlier: 6.386A  pdb=" N   ALA A  49 " --> pdb=" O   ALA A  80 " (cutoff:3.500A)
      removed outlier: 8.952A  pdb=" N   VAL A  82 " --> pdb=" O   ALA A  49 " (cutoff:3.500A)
      removed outlier: 6.135A  pdb=" N   ILE A 165 " --> pdb=" O   GLY A 189 " (cutoff:3.500A)
      removed outlier: 6.104A  pdb=" N   GLU A 164 " --> pdb=" O   MET A 160 " (cutoff:3.500A)
      removed outlier: 6.354A  pdb=" N   MET A 160 " --> pdb=" O   GLU A 164 " (cutoff:3.500A)
      removed outlier: 3.707A  pdb=" N   THR A 166 " --> pdb=" O   VAL A 158 " (cutoff:3.500A)
      removed outlier: 6.598A  pdb=" N   TRP A 152 " --> pdb=" O   GLN A 172 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 49 through 50
      removed outlier: 6.386A  pdb=" N   ALA A  49 " --> pdb=" O   ALA A  80 " (cutoff:3.500A)
      removed outlier: 8.952A  pdb=" N   VAL A  82 " --> pdb=" O   ALA A  49 " (cutoff:3.500A)
      removed outlier: 6.135A  pdb=" N   ILE A 165 " --> pdb=" O   GLY A 189 " (cutoff:3.500A)
      removed outlier: 6.104A  pdb=" N   GLU A 164 " --> pdb=" O   MET A 160 " (cutoff:3.500A)
      removed outlier: 6.354A  pdb=" N   MET A 160 " --> pdb=" O   GLU A 164 " (cutoff:3.500A)
      removed outlier: 3.707A  pdb=" N   THR A 166 " --> pdb=" O   VAL A 158 " (cutoff:3.500A)
      removed outlier: 6.598A  pdb=" N   TRP A 152 " --> pdb=" O   GLN A 172 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   GLY A 153 " --> pdb=" O   TRP A 144 " (cutoff:3.500A)
      removed outlier: 3.558A  pdb=" N   TRP A 144 " --> pdb=" O   GLY A 153 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 207 through 209
    Processing sheet with id=AA4, first strand: chain 'A' and resid 383 through 388
      removed outlier: 4.223A  pdb=" N   ASN A 398 " --> pdb=" O   ARG A 342 " (cutoff:3.500A)
      removed outlier: 4.908A  pdb=" N   ARG A 342 " --> pdb=" O   ASN A 398 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 513 through 514
      removed outlier: 3.605A  pdb=" N   PHE A 514 " --> pdb=" O   ILE A 517 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 522 through 523
    Processing sheet with id=AA7, first strand: chain 'A' and resid 575 through 577
      removed outlier: 6.923A  pdb=" N   PHE A 624 " --> pdb=" O   CYS A 637 " (cutoff:3.500A)
      removed outlier: 7.047A  pdb=" N   CYS A 637 " --> pdb=" O   PHE A 624 " (cutoff:3.500A)
      removed outlier: 5.247A  pdb=" N   VAL A 626 " --> pdb=" O   LEU A 635 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 689 through 691
      removed outlier: 3.578A  pdb=" N   HIS A 691 " --> pdb=" O   GLY A 695 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 49 through 50
      removed outlier: 6.345A  pdb=" N   ALA B  49 " --> pdb=" O   ALA B  80 " (cutoff:3.500A)
      removed outlier: 8.930A  pdb=" N   VAL B  82 " --> pdb=" O   ALA B  49 " (cutoff:3.500A)
      removed outlier: 6.146A  pdb=" N   ILE B 165 " --> pdb=" O   GLY B 189 " (cutoff:3.500A)
      removed outlier: 6.055A  pdb=" N   GLU B 164 " --> pdb=" O   MET B 160 " (cutoff:3.500A)
      removed outlier: 6.391A  pdb=" N   MET B 160 " --> pdb=" O   GLU B 164 " (cutoff:3.500A)
      removed outlier: 3.713A  pdb=" N   THR B 166 " --> pdb=" O   VAL B 158 " (cutoff:3.500A)
      removed outlier: 6.697A  pdb=" N   TRP B 152 " --> pdb=" O   GLN B 172 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 49 through 50
      removed outlier: 6.345A  pdb=" N   ALA B  49 " --> pdb=" O   ALA B  80 " (cutoff:3.500A)
      removed outlier: 8.930A  pdb=" N   VAL B  82 " --> pdb=" O   ALA B  49 " (cutoff:3.500A)
      removed outlier: 6.146A  pdb=" N   ILE B 165 " --> pdb=" O   GLY B 189 " (cutoff:3.500A)
      removed outlier: 6.055A  pdb=" N   GLU B 164 " --> pdb=" O   MET B 160 " (cutoff:3.500A)
      removed outlier: 6.391A  pdb=" N   MET B 160 " --> pdb=" O   GLU B 164 " (cutoff:3.500A)
      removed outlier: 3.713A  pdb=" N   THR B 166 " --> pdb=" O   VAL B 158 " (cutoff:3.500A)
      removed outlier: 6.697A  pdb=" N   TRP B 152 " --> pdb=" O   GLN B 172 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   GLY B 153 " --> pdb=" O   TRP B 144 " (cutoff:3.500A)
      removed outlier: 3.581A  pdb=" N   TRP B 144 " --> pdb=" O   GLY B 153 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 207 through 209
    Processing sheet with id=AB3, first strand: chain 'B' and resid 383 through 388
      removed outlier: 4.202A  pdb=" N   ASN B 398 " --> pdb=" O   ARG B 342 " (cutoff:3.500A)
      removed outlier: 4.954A  pdb=" N   ARG B 342 " --> pdb=" O   ASN B 398 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'B' and resid 513 through 514
      removed outlier: 3.599A  pdb=" N   PHE B 514 " --> pdb=" O   ILE B 517 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'B' and resid 522 through 524
    Processing sheet with id=AB6, first strand: chain 'B' and resid 575 through 577
      removed outlier: 6.994A  pdb=" N   PHE B 624 " --> pdb=" O   CYS B 637 " (cutoff:3.500A)
      removed outlier: 7.115A  pdb=" N   CYS B 637 " --> pdb=" O   PHE B 624 " (cutoff:3.500A)
      removed outlier: 5.324A  pdb=" N   VAL B 626 " --> pdb=" O   LEU B 635 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'B' and resid 689 through 691
      removed outlier: 3.710A  pdb=" N   HIS B 691 " --> pdb=" O   GLY B 695 " (cutoff:3.500A)

    723 hydrogen bonds defined for protein.
    2058 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 5.86

  Time building geometry restraints manager: 3.87 seconds

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

  Histogram of bond lengths:
        1.14 -     1.27: 2035
        1.27 -     1.41: 2971
        1.41 -     1.54: 7217
        1.54 -     1.68: 15
        1.68 -     1.81: 82
  Bond restraints: 12320
  Sorted by residual:
  bond pdb=" C   TYR B 208 "
       pdb=" O   TYR B 208 "
    ideal  model  delta    sigma   weight residual
    1.236  1.140  0.097 1.15e-02 7.56e+03 7.05e+01
  bond pdb=" C   GLN A  33 "
       pdb=" N   GLN A  34 "
    ideal  model  delta    sigma   weight residual
    1.335  1.269  0.066 1.36e-02 5.41e+03 2.35e+01
  bond pdb=" C   GLN A  33 "
       pdb=" O   GLN A  33 "
    ideal  model  delta    sigma   weight residual
    1.236  1.181  0.054 1.29e-02 6.01e+03 1.78e+01
  bond pdb=" CA  THR B 209 "
       pdb=" C   THR B 209 "
    ideal  model  delta    sigma   weight residual
    1.522  1.470  0.051 1.24e-02 6.50e+03 1.72e+01
  bond pdb=" C   THR B 209 "
       pdb=" N   LYS B 210 "
    ideal  model  delta    sigma   weight residual
    1.332  1.278  0.055 1.40e-02 5.10e+03 1.52e+01
  ... (remaining 12315 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.99: 15922
        1.99 -     3.99: 626
        3.99 -     5.98: 130
        5.98 -     7.97: 21
        7.97 -     9.97: 5
  Bond angle restraints: 16704
  Sorted by residual:
  angle pdb=" N   GLY A 807 "
        pdb=" CA  GLY A 807 "
        pdb=" C   GLY A 807 "
      ideal   model   delta    sigma   weight residual
     111.85  120.10   -8.25 1.20e+00 6.94e-01 4.73e+01
  angle pdb=" N   GLY B 807 "
        pdb=" CA  GLY B 807 "
        pdb=" C   GLY B 807 "
      ideal   model   delta    sigma   weight residual
     111.63  118.57   -6.94 1.15e+00 7.56e-01 3.64e+01
  angle pdb=" CA  GLY B 807 "
        pdb=" C   GLY B 807 "
        pdb=" O   GLY B 807 "
      ideal   model   delta    sigma   weight residual
     122.16  117.36    4.80 8.20e-01 1.49e+00 3.43e+01
  angle pdb=" CA  GLY A 807 "
        pdb=" C   GLY A 807 "
        pdb=" O   GLY A 807 "
      ideal   model   delta    sigma   weight residual
     122.13  117.20    4.93 8.90e-01 1.26e+00 3.07e+01
  angle pdb=" N   ASP A 673 "
        pdb=" CA  ASP A 673 "
        pdb=" C   ASP A 673 "
      ideal   model   delta    sigma   weight residual
     112.93  106.76    6.17 1.12e+00 7.97e-01 3.04e+01
  ... (remaining 16699 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.55: 6694
       17.55 -    35.10: 537
       35.10 -    52.65: 139
       52.65 -    70.20: 44
       70.20 -    87.76: 8
  Dihedral angle restraints: 7422
    sinusoidal: 3004
      harmonic: 4418
  Sorted by residual:
  dihedral pdb=" CA  LYS B 647 "
           pdb=" C   LYS B 647 "
           pdb=" N   GLU B 648 "
           pdb=" CA  GLU B 648 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -156.35  -23.65     0      5.00e+00 4.00e-02 2.24e+01
  dihedral pdb=" CA  LYS A 647 "
           pdb=" C   LYS A 647 "
           pdb=" N   GLU A 648 "
           pdb=" CA  GLU A 648 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -156.38  -23.62     0      5.00e+00 4.00e-02 2.23e+01
  dihedral pdb=" C   MET A 672 "
           pdb=" N   MET A 672 "
           pdb=" CA  MET A 672 "
           pdb=" CB  MET A 672 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -111.28  -11.32     0      2.50e+00 1.60e-01 2.05e+01
  ... (remaining 7419 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.062: 1510
       0.062 -    0.125: 315
       0.125 -    0.187: 46
       0.187 -    0.250: 16
       0.250 -    0.312: 7
  Chirality restraints: 1894
  Sorted by residual:
  chirality pdb=" CB  THR B 209 "
            pdb=" CA  THR B 209 "
            pdb=" OG1 THR B 209 "
            pdb=" CG2 THR B 209 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.24    0.31 2.00e-01 2.50e+01 2.43e+00
  chirality pdb=" CB  THR A 209 "
            pdb=" CA  THR A 209 "
            pdb=" OG1 THR A 209 "
            pdb=" CG2 THR A 209 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.24    0.31 2.00e-01 2.50e+01 2.40e+00
  chirality pdb=" CA  THR B 209 "
            pdb=" N   THR B 209 "
            pdb=" C   THR B 209 "
            pdb=" CB  THR B 209 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.24    0.28 2.00e-01 2.50e+01 1.99e+00
  ... (remaining 1891 not shown)

  Planarity restraints: 2158
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 208 "   -0.058 2.00e-02 2.50e+03   3.04e-02 1.85e+01
        pdb=" CG  TYR A 208 "    0.035 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 208 "    0.026 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 208 "    0.014 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 208 "    0.007 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 208 "    0.013 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 208 "    0.004 2.00e-02 2.50e+03
        pdb=" OH  TYR A 208 "   -0.041 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR B 208 "    0.054 2.00e-02 2.50e+03   2.88e-02 1.66e+01
        pdb=" CG  TYR B 208 "   -0.028 2.00e-02 2.50e+03
        pdb=" CD1 TYR B 208 "   -0.028 2.00e-02 2.50e+03
        pdb=" CD2 TYR B 208 "   -0.013 2.00e-02 2.50e+03
        pdb=" CE1 TYR B 208 "   -0.006 2.00e-02 2.50e+03
        pdb=" CE2 TYR B 208 "   -0.015 2.00e-02 2.50e+03
        pdb=" CZ  TYR B 208 "   -0.006 2.00e-02 2.50e+03
        pdb=" OH  TYR B 208 "    0.041 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLN A  33 "    0.020 2.00e-02 2.50e+03   4.04e-02 1.63e+01
        pdb=" C   GLN A  33 "   -0.070 2.00e-02 2.50e+03
        pdb=" O   GLN A  33 "    0.025 2.00e-02 2.50e+03
        pdb=" N   GLN A  34 "    0.025 2.00e-02 2.50e+03
  ... (remaining 2155 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 1232
        2.74 -     3.28: 11948
        3.28 -     3.82: 19021
        3.82 -     4.36: 22739
        4.36 -     4.90: 39436
  Nonbonded interactions: 94376
  Sorted by model distance:
  nonbonded pdb=" OE1 GLU A 347 "
            pdb=" OH  TYR A 542 "
     model   vdw
     2.197 3.040
  nonbonded pdb=" O   LEU A  30 "
            pdb=" NE2 GLN A 198 "
     model   vdw
     2.198 3.120
  nonbonded pdb=" O   ASN B 833 "
            pdb=" NZ  LYS B 835 "
     model   vdw
     2.207 3.120
  nonbonded pdb=" OG1 THR A 350 "
            pdb=" O   GLU A 351 "
     model   vdw
     2.212 3.040
  nonbonded pdb=" OE1 GLU B 347 "
            pdb=" OH  TYR B 542 "
     model   vdw
     2.217 3.040
  ... (remaining 94371 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 28 through 679 or (resid 680 and (name N or name CA or nam \ 
e C or name O or name CB )) or resid 681 through 874))
  selection = (chain 'B' and (resid 28 through 820 or (resid 821 and (name N or name CA or nam \ 
e C or name O or name CB )) or resid 822 through 874))
}

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:             3.180
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.450
  Check model and map are aligned:         0.090
  Set scattering table:                    0.110
  Process input model:                     34.580
  Find NCS groups from input model:        0.480
  Set up NCS constraints:                  0.060
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:3.060
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   42.020
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6956
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      :  0.007   0.097  12320  Z= 0.412
  Angle     :  0.936   9.965  16704  Z= 0.617
  Chirality :  0.057   0.312   1894
  Planarity :  0.006   0.053   2158
  Dihedral  : 14.445  87.755   4566
  Min Nonbonded Distance : 2.197

Molprobity Statistics.
  All-atom Clashscore : 9.77
  Ramachandran Plot:
    Outliers :  0.33 %
    Allowed  :  4.16 %
    Favored  : 95.51 %
  Rotamer:
    Outliers :  7.59 %
    Allowed  : 10.93 %
    Favored  : 81.49 %
  Cbeta Deviations :  0.21 %
  Peptide Plane:
    Cis-proline     : 8.82 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.02 (0.21), residues: 1514
  helix:  0.99 (0.19), residues: 750
  sheet: -0.53 (0.37), residues: 184
  loop : -1.12 (0.25), residues: 580

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.002   TRP A  43 
 HIS   0.007   0.001   HIS A 356 
 PHE   0.017   0.002   PHE A 668 
 TYR   0.058   0.004   TYR A 208 
 ARG   0.004   0.000   ARG B 561 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.15532 (  669)
  hydrogen bonds       : angle       6.37844 ( 2058)
  covalent geometry    : bond        0.00724 (12320)
  covalent geometry    : angle       0.93556 (16704)

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

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

  3028 Ramachandran restraints generated.
    1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3028 Ramachandran restraints generated.
    1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  332 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 100
    poor density    : 232
  time to evaluate  : 1.211 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   30 LEU cc_start: 0.8139 (OUTLIER) cc_final: 0.7584 (mp)
REVERT: A  125 LEU cc_start: 0.8054 (OUTLIER) cc_final: 0.7423 (mp)
REVERT: A  253 LEU cc_start: 0.6498 (mt) cc_final: 0.6295 (mt)
REVERT: A  263 ASP cc_start: 0.8084 (t70) cc_final: 0.7757 (t0)
REVERT: B   30 LEU cc_start: 0.7928 (OUTLIER) cc_final: 0.7448 (mp)
REVERT: B  118 GLN cc_start: 0.7674 (OUTLIER) cc_final: 0.7407 (mt0)
REVERT: B  183 SER cc_start: 0.9243 (OUTLIER) cc_final: 0.8981 (p)
REVERT: B  253 LEU cc_start: 0.6500 (mt) cc_final: 0.6260 (mt)
REVERT: B  263 ASP cc_start: 0.7974 (t70) cc_final: 0.7655 (t0)
REVERT: B  366 GLU cc_start: 0.7707 (tt0) cc_final: 0.7468 (tt0)
REVERT: B  500 TRP cc_start: 0.6813 (OUTLIER) cc_final: 0.5403 (p-90)
  outliers start: 100
  outliers final: 48
  residues processed: 324
  average time/residue: 0.3062
  time to fit residues: 137.4262
Evaluate side-chains
  189 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 135
  time to evaluate  : 1.349 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   30 LEU
Chi-restraints excluded: chain A residue   33 GLN
Chi-restraints excluded: chain A residue   41 ASP
Chi-restraints excluded: chain A residue   53 CYS
Chi-restraints excluded: chain A residue   79 VAL
Chi-restraints excluded: chain A residue  125 LEU
Chi-restraints excluded: chain A residue  126 SER
Chi-restraints excluded: chain A residue  132 VAL
Chi-restraints excluded: chain A residue  161 ASP
Chi-restraints excluded: chain A residue  185 GLU
Chi-restraints excluded: chain A residue  196 SER
Chi-restraints excluded: chain A residue  200 VAL
Chi-restraints excluded: chain A residue  209 THR
Chi-restraints excluded: chain A residue  221 ASN
Chi-restraints excluded: chain A residue  236 ASP
Chi-restraints excluded: chain A residue  259 ILE
Chi-restraints excluded: chain A residue  277 SER
Chi-restraints excluded: chain A residue  307 THR
Chi-restraints excluded: chain A residue  350 THR
Chi-restraints excluded: chain A residue  388 THR
Chi-restraints excluded: chain A residue  470 THR
Chi-restraints excluded: chain A residue  529 SER
Chi-restraints excluded: chain A residue  598 ILE
Chi-restraints excluded: chain A residue  640 THR
Chi-restraints excluded: chain A residue  650 VAL
Chi-restraints excluded: chain A residue  740 ILE
Chi-restraints excluded: chain A residue  741 VAL
Chi-restraints excluded: chain A residue  750 ILE
Chi-restraints excluded: chain A residue  811 SER
Chi-restraints excluded: chain B residue   30 LEU
Chi-restraints excluded: chain B residue   41 ASP
Chi-restraints excluded: chain B residue   53 CYS
Chi-restraints excluded: chain B residue   79 VAL
Chi-restraints excluded: chain B residue  118 GLN
Chi-restraints excluded: chain B residue  126 SER
Chi-restraints excluded: chain B residue  132 VAL
Chi-restraints excluded: chain B residue  161 ASP
Chi-restraints excluded: chain B residue  183 SER
Chi-restraints excluded: chain B residue  185 GLU
Chi-restraints excluded: chain B residue  200 VAL
Chi-restraints excluded: chain B residue  209 THR
Chi-restraints excluded: chain B residue  221 ASN
Chi-restraints excluded: chain B residue  259 ILE
Chi-restraints excluded: chain B residue  277 SER
Chi-restraints excluded: chain B residue  350 THR
Chi-restraints excluded: chain B residue  388 THR
Chi-restraints excluded: chain B residue  500 TRP
Chi-restraints excluded: chain B residue  529 SER
Chi-restraints excluded: chain B residue  555 MET
Chi-restraints excluded: chain B residue  626 VAL
Chi-restraints excluded: chain B residue  640 THR
Chi-restraints excluded: chain B residue  650 VAL
Chi-restraints excluded: chain B residue  741 VAL
Chi-restraints excluded: chain B residue  813 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 128 optimal weight:    0.9980
   chunk 115 optimal weight:    1.9990
   chunk 63 optimal weight:    4.9990
   chunk 39 optimal weight:    5.9990
   chunk 77 optimal weight:    0.7980
   chunk 61 optimal weight:   10.0000
   chunk 119 optimal weight:    0.6980
   chunk 46 optimal weight:    6.9990
   chunk 72 optimal weight:    5.9990
   chunk 88 optimal weight:    6.9990
   chunk 138 optimal weight:    1.9990
   overall best weight:    1.2984

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

Flipped N/Q/H residues before XYZ refinement:
A  98 ASN
A 809 GLN
B  33 GLN
B  98 ASN
B 198 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4110 r_free = 0.4110 target = 0.171922 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3776 r_free = 0.3776 target = 0.141974 restraints weight = 19614.255|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3745 r_free = 0.3745 target = 0.140693 restraints weight = 14865.249|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3750 r_free = 0.3750 target = 0.141457 restraints weight = 14442.644|
|-----------------------------------------------------------------------------|
r_work (final): 0.3749
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7300
moved from start:          0.2359

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.058  12320  Z= 0.146
  Angle     :  0.588   7.102  16704  Z= 0.315
  Chirality :  0.044   0.158   1894
  Planarity :  0.005   0.047   2158
  Dihedral  :  8.302  67.590   1727
  Min Nonbonded Distance : 2.466

Molprobity Statistics.
  All-atom Clashscore : 7.87
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  2.64 %
    Favored  : 97.29 %
  Rotamer:
    Outliers :  3.79 %
    Allowed  : 16.16 %
    Favored  : 80.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.82 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.47 (0.22), residues: 1514
  helix:  1.35 (0.19), residues: 772
  sheet: -0.19 (0.39), residues: 178
  loop : -0.93 (0.26), residues: 564

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A  43 
 HIS   0.003   0.001   HIS A 544 
 PHE   0.014   0.001   PHE B 534 
 TYR   0.018   0.002   TYR A 188 
 ARG   0.004   0.000   ARG A 682 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05491 (  669)
  hydrogen bonds       : angle       4.72058 ( 2058)
  covalent geometry    : bond        0.00313 (12320)
  covalent geometry    : angle       0.58779 (16704)

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

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

  3028 Ramachandran restraints generated.
    1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3028 Ramachandran restraints generated.
    1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  213 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 163
  time to evaluate  : 1.404 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  125 LEU cc_start: 0.8106 (OUTLIER) cc_final: 0.7678 (mp)
REVERT: A  253 LEU cc_start: 0.6546 (mt) cc_final: 0.6320 (mt)
REVERT: A  744 PHE cc_start: 0.7706 (m-80) cc_final: 0.7153 (m-80)
REVERT: B   30 LEU cc_start: 0.7741 (OUTLIER) cc_final: 0.7250 (mp)
REVERT: B  183 SER cc_start: 0.8964 (OUTLIER) cc_final: 0.8665 (p)
REVERT: B  253 LEU cc_start: 0.6635 (mt) cc_final: 0.6380 (mt)
REVERT: B  672 MET cc_start: 0.7519 (tmm) cc_final: 0.6940 (tmm)
REVERT: B  684 GLN cc_start: 0.6957 (mp10) cc_final: 0.6639 (mp10)
REVERT: B  697 MET cc_start: 0.6868 (mtp) cc_final: 0.6644 (mtp)
  outliers start: 50
  outliers final: 25
  residues processed: 200
  average time/residue: 0.2468
  time to fit residues: 70.7125
Evaluate side-chains
  159 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 131
  time to evaluate  : 1.309 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 ILE
Chi-restraints excluded: chain A residue   79 VAL
Chi-restraints excluded: chain A residue  117 SER
Chi-restraints excluded: chain A residue  125 LEU
Chi-restraints excluded: chain A residue  132 VAL
Chi-restraints excluded: chain A residue  196 SER
Chi-restraints excluded: chain A residue  221 ASN
Chi-restraints excluded: chain A residue  236 ASP
Chi-restraints excluded: chain A residue  259 ILE
Chi-restraints excluded: chain A residue  315 LEU
Chi-restraints excluded: chain A residue  388 THR
Chi-restraints excluded: chain A residue  470 THR
Chi-restraints excluded: chain A residue  640 THR
Chi-restraints excluded: chain A residue  750 ILE
Chi-restraints excluded: chain B residue   30 LEU
Chi-restraints excluded: chain B residue   36 ILE
Chi-restraints excluded: chain B residue   53 CYS
Chi-restraints excluded: chain B residue   79 VAL
Chi-restraints excluded: chain B residue  132 VAL
Chi-restraints excluded: chain B residue  183 SER
Chi-restraints excluded: chain B residue  185 GLU
Chi-restraints excluded: chain B residue  221 ASN
Chi-restraints excluded: chain B residue  259 ILE
Chi-restraints excluded: chain B residue  350 THR
Chi-restraints excluded: chain B residue  388 THR
Chi-restraints excluded: chain B residue  470 THR
Chi-restraints excluded: chain B residue  640 THR
Chi-restraints excluded: chain B residue  826 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 57 optimal weight:    4.9990
   chunk 105 optimal weight:    9.9990
   chunk 55 optimal weight:    1.9990
   chunk 43 optimal weight:    0.6980
   chunk 83 optimal weight:    7.9990
   chunk 16 optimal weight:    6.9990
   chunk 129 optimal weight:    2.9990
   chunk 144 optimal weight:   10.0000
   chunk 113 optimal weight:    7.9990
   chunk 81 optimal weight:    2.9990
   chunk 92 optimal weight:    0.8980
   overall best weight:    1.9186

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

Flipped N/Q/H residues before XYZ refinement:
** A 809 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4094 r_free = 0.4094 target = 0.170719 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3765 r_free = 0.3765 target = 0.141559 restraints weight = 20230.774|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3743 r_free = 0.3743 target = 0.140998 restraints weight = 15932.674|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3746 r_free = 0.3746 target = 0.141748 restraints weight = 14730.494|
|-----------------------------------------------------------------------------|
r_work (final): 0.3745
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7321
moved from start:          0.2911

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.082  12320  Z= 0.158
  Angle     :  0.569   7.332  16704  Z= 0.304
  Chirality :  0.044   0.154   1894
  Planarity :  0.005   0.051   2158
  Dihedral  :  6.660  59.564   1679
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 7.87
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  3.70 %
    Favored  : 96.24 %
  Rotamer:
    Outliers :  3.41 %
    Allowed  : 17.98 %
    Favored  : 78.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.82 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.67 (0.22), residues: 1514
  helix:  1.62 (0.19), residues: 754
  sheet: -0.04 (0.40), residues: 174
  loop : -0.96 (0.25), residues: 586

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A  43 
 HIS   0.006   0.001   HIS B 544 
 PHE   0.016   0.001   PHE A 804 
 TYR   0.019   0.002   TYR A 188 
 ARG   0.005   0.000   ARG B 391 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05185 (  669)
  hydrogen bonds       : angle       4.48661 ( 2058)
  covalent geometry    : bond        0.00362 (12320)
  covalent geometry    : angle       0.56926 (16704)

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

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

  3028 Ramachandran restraints generated.
    1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3028 Ramachandran restraints generated.
    1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  192 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 147
  time to evaluate  : 1.413 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  125 LEU cc_start: 0.8152 (OUTLIER) cc_final: 0.7735 (mp)
REVERT: A  253 LEU cc_start: 0.6552 (mt) cc_final: 0.6306 (mt)
REVERT: A  668 PHE cc_start: 0.7387 (t80) cc_final: 0.7045 (t80)
REVERT: A  744 PHE cc_start: 0.7630 (m-80) cc_final: 0.7092 (m-80)
REVERT: B  253 LEU cc_start: 0.6698 (mt) cc_final: 0.6416 (mt)
REVERT: B  639 ILE cc_start: 0.7898 (OUTLIER) cc_final: 0.7601 (mp)
REVERT: B  672 MET cc_start: 0.7432 (tmm) cc_final: 0.6854 (tmm)
REVERT: B  697 MET cc_start: 0.6653 (mtp) cc_final: 0.6258 (mtp)
REVERT: B  701 MET cc_start: 0.7897 (mmm) cc_final: 0.7625 (mmm)
REVERT: B  744 PHE cc_start: 0.7318 (m-80) cc_final: 0.6884 (m-80)
  outliers start: 45
  outliers final: 29
  residues processed: 185
  average time/residue: 0.2347
  time to fit residues: 63.7119
Evaluate side-chains
  154 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 123
  time to evaluate  : 1.458 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 ILE
Chi-restraints excluded: chain A residue   79 VAL
Chi-restraints excluded: chain A residue  117 SER
Chi-restraints excluded: chain A residue  125 LEU
Chi-restraints excluded: chain A residue  132 VAL
Chi-restraints excluded: chain A residue  161 ASP
Chi-restraints excluded: chain A residue  185 GLU
Chi-restraints excluded: chain A residue  196 SER
Chi-restraints excluded: chain A residue  221 ASN
Chi-restraints excluded: chain A residue  236 ASP
Chi-restraints excluded: chain A residue  315 LEU
Chi-restraints excluded: chain A residue  372 ILE
Chi-restraints excluded: chain A residue  388 THR
Chi-restraints excluded: chain A residue  470 THR
Chi-restraints excluded: chain A residue  533 ASN
Chi-restraints excluded: chain A residue  598 ILE
Chi-restraints excluded: chain A residue  640 THR
Chi-restraints excluded: chain A residue  750 ILE
Chi-restraints excluded: chain B residue   36 ILE
Chi-restraints excluded: chain B residue   79 VAL
Chi-restraints excluded: chain B residue  132 VAL
Chi-restraints excluded: chain B residue  221 ASN
Chi-restraints excluded: chain B residue  236 ASP
Chi-restraints excluded: chain B residue  372 ILE
Chi-restraints excluded: chain B residue  375 LYS
Chi-restraints excluded: chain B residue  388 THR
Chi-restraints excluded: chain B residue  470 THR
Chi-restraints excluded: chain B residue  639 ILE
Chi-restraints excluded: chain B residue  640 THR
Chi-restraints excluded: chain B residue  741 VAL
Chi-restraints excluded: chain B residue  826 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 64 optimal weight:    1.9990
   chunk 99 optimal weight:    0.0870
   chunk 52 optimal weight:    0.3980
   chunk 58 optimal weight:    7.9990
   chunk 107 optimal weight:    4.9990
   chunk 147 optimal weight:    8.9990
   chunk 94 optimal weight:    1.9990
   chunk 56 optimal weight:   10.0000
   chunk 93 optimal weight:    2.9990
   chunk 149 optimal weight:    5.9990
   chunk 38 optimal weight:    0.6980
   overall best weight:    1.0362

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

Flipped N/Q/H residues before XYZ refinement:
A 118 GLN
A 618 GLN
A 809 GLN
** B 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 684 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4115 r_free = 0.4115 target = 0.172728 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3785 r_free = 0.3785 target = 0.143275 restraints weight = 19816.473|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3781 r_free = 0.3781 target = 0.143395 restraints weight = 14395.737|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3778 r_free = 0.3778 target = 0.143508 restraints weight = 16005.597|
|-----------------------------------------------------------------------------|
r_work (final): 0.3778
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7276
moved from start:          0.3349

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.058  12320  Z= 0.116
  Angle     :  0.515   7.794  16704  Z= 0.272
  Chirality :  0.042   0.143   1894
  Planarity :  0.004   0.045   2158
  Dihedral  :  5.752  58.711   1667
  Min Nonbonded Distance : 2.582

Molprobity Statistics.
  All-atom Clashscore : 6.46
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  2.84 %
    Favored  : 97.09 %
  Rotamer:
    Outliers :  3.57 %
    Allowed  : 18.59 %
    Favored  : 77.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.82 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.93 (0.22), residues: 1514
  helix:  1.77 (0.19), residues: 762
  sheet:  0.06 (0.40), residues: 182
  loop : -0.76 (0.26), residues: 570

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A  43 
 HIS   0.002   0.001   HIS B 264 
 PHE   0.009   0.001   PHE B 534 
 TYR   0.014   0.001   TYR A 188 
 ARG   0.009   0.000   ARG A 796 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04152 (  669)
  hydrogen bonds       : angle       4.16081 ( 2058)
  covalent geometry    : bond        0.00254 (12320)
  covalent geometry    : angle       0.51453 (16704)

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

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

  3028 Ramachandran restraints generated.
    1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3028 Ramachandran restraints generated.
    1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  194 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 147
  time to evaluate  : 1.325 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  125 LEU cc_start: 0.8142 (OUTLIER) cc_final: 0.7768 (mp)
REVERT: A  253 LEU cc_start: 0.6353 (mt) cc_final: 0.6083 (mt)
REVERT: A  634 LEU cc_start: 0.8755 (mm) cc_final: 0.8398 (mt)
REVERT: A  639 ILE cc_start: 0.8048 (OUTLIER) cc_final: 0.7761 (mp)
REVERT: A  668 PHE cc_start: 0.7419 (t80) cc_final: 0.6977 (t80)
REVERT: A  672 MET cc_start: 0.7141 (ttm) cc_final: 0.6801 (tmm)
REVERT: A  701 MET cc_start: 0.6406 (mmm) cc_final: 0.6142 (mmm)
REVERT: A  744 PHE cc_start: 0.7603 (m-80) cc_final: 0.7121 (m-80)
REVERT: B  253 LEU cc_start: 0.6518 (mt) cc_final: 0.6219 (mt)
REVERT: B  391 ARG cc_start: 0.7461 (mtm110) cc_final: 0.6528 (mtp85)
REVERT: B  672 MET cc_start: 0.7385 (tmm) cc_final: 0.6773 (tmm)
REVERT: B  697 MET cc_start: 0.6539 (mtp) cc_final: 0.6316 (mtp)
  outliers start: 47
  outliers final: 30
  residues processed: 186
  average time/residue: 0.2485
  time to fit residues: 68.5139
Evaluate side-chains
  166 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 134
  time to evaluate  : 1.308 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 ILE
Chi-restraints excluded: chain A residue   53 CYS
Chi-restraints excluded: chain A residue   79 VAL
Chi-restraints excluded: chain A residue  125 LEU
Chi-restraints excluded: chain A residue  132 VAL
Chi-restraints excluded: chain A residue  221 ASN
Chi-restraints excluded: chain A residue  236 ASP
Chi-restraints excluded: chain A residue  315 LEU
Chi-restraints excluded: chain A residue  375 LYS
Chi-restraints excluded: chain A residue  388 THR
Chi-restraints excluded: chain A residue  544 HIS
Chi-restraints excluded: chain A residue  598 ILE
Chi-restraints excluded: chain A residue  639 ILE
Chi-restraints excluded: chain A residue  640 THR
Chi-restraints excluded: chain A residue  646 ILE
Chi-restraints excluded: chain A residue  750 ILE
Chi-restraints excluded: chain A residue  845 LEU
Chi-restraints excluded: chain B residue   36 ILE
Chi-restraints excluded: chain B residue   79 VAL
Chi-restraints excluded: chain B residue  132 VAL
Chi-restraints excluded: chain B residue  221 ASN
Chi-restraints excluded: chain B residue  236 ASP
Chi-restraints excluded: chain B residue  315 LEU
Chi-restraints excluded: chain B residue  375 LYS
Chi-restraints excluded: chain B residue  470 THR
Chi-restraints excluded: chain B residue  551 ILE
Chi-restraints excluded: chain B residue  598 ILE
Chi-restraints excluded: chain B residue  640 THR
Chi-restraints excluded: chain B residue  650 VAL
Chi-restraints excluded: chain B residue  750 ILE
Chi-restraints excluded: chain B residue  813 THR
Chi-restraints excluded: chain B residue  826 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 57 optimal weight:    0.9980
   chunk 132 optimal weight:    5.9990
   chunk 143 optimal weight:    0.7980
   chunk 90 optimal weight:    0.8980
   chunk 24 optimal weight:    4.9990
   chunk 124 optimal weight:    4.9990
   chunk 65 optimal weight:    8.9990
   chunk 60 optimal weight:    8.9990
   chunk 150 optimal weight:    1.9990
   chunk 72 optimal weight:    0.9990
   chunk 63 optimal weight:    6.9990
   overall best weight:    1.1384

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

Flipped N/Q/H residues before XYZ refinement:
A 833 ASN
** B 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4113 r_free = 0.4113 target = 0.172535 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3781 r_free = 0.3781 target = 0.142854 restraints weight = 19846.065|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3760 r_free = 0.3760 target = 0.141690 restraints weight = 14331.985|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3765 r_free = 0.3765 target = 0.142486 restraints weight = 15039.122|
|-----------------------------------------------------------------------------|
r_work (final): 0.3762
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7308
moved from start:          0.3589

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048  12320  Z= 0.116
  Angle     :  0.509   7.619  16704  Z= 0.269
  Chirality :  0.042   0.175   1894
  Planarity :  0.004   0.046   2158
  Dihedral  :  5.391  58.148   1664
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 6.50
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  3.30 %
    Favored  : 96.63 %
  Rotamer:
    Outliers :  3.95 %
    Allowed  : 18.36 %
    Favored  : 77.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.82 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.07 (0.22), residues: 1514
  helix:  1.82 (0.19), residues: 766
  sheet:  0.14 (0.40), residues: 182
  loop : -0.62 (0.26), residues: 566

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B  43 
 HIS   0.003   0.001   HIS B 264 
 PHE   0.009   0.001   PHE B 168 
 TYR   0.016   0.001   TYR A 188 
 ARG   0.007   0.000   ARG A 796 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04104 (  669)
  hydrogen bonds       : angle       4.05658 ( 2058)
  covalent geometry    : bond        0.00253 (12320)
  covalent geometry    : angle       0.50879 (16704)

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

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

  3028 Ramachandran restraints generated.
    1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3028 Ramachandran restraints generated.
    1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  196 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 144
  time to evaluate  : 1.444 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  253 LEU cc_start: 0.6341 (mt) cc_final: 0.6079 (mt)
REVERT: A  639 ILE cc_start: 0.8053 (OUTLIER) cc_final: 0.7800 (mp)
REVERT: A  668 PHE cc_start: 0.7509 (t80) cc_final: 0.7106 (t80)
REVERT: A  672 MET cc_start: 0.6897 (ttm) cc_final: 0.6611 (tmm)
REVERT: A  701 MET cc_start: 0.6418 (mmm) cc_final: 0.6173 (mmm)
REVERT: A  744 PHE cc_start: 0.7730 (m-80) cc_final: 0.6929 (m-80)
REVERT: B  253 LEU cc_start: 0.6494 (mt) cc_final: 0.6218 (mt)
REVERT: B  639 ILE cc_start: 0.7874 (OUTLIER) cc_final: 0.7621 (mp)
REVERT: B  672 MET cc_start: 0.7363 (tmm) cc_final: 0.6727 (tmm)
REVERT: B  697 MET cc_start: 0.6529 (mtp) cc_final: 0.6260 (mtp)
REVERT: B  744 PHE cc_start: 0.7377 (m-80) cc_final: 0.6930 (m-80)
  outliers start: 52
  outliers final: 29
  residues processed: 185
  average time/residue: 0.2746
  time to fit residues: 74.3640
Evaluate side-chains
  164 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 133
  time to evaluate  : 1.981 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 ILE
Chi-restraints excluded: chain A residue   53 CYS
Chi-restraints excluded: chain A residue   79 VAL
Chi-restraints excluded: chain A residue  117 SER
Chi-restraints excluded: chain A residue  132 VAL
Chi-restraints excluded: chain A residue  315 LEU
Chi-restraints excluded: chain A residue  388 THR
Chi-restraints excluded: chain A residue  470 THR
Chi-restraints excluded: chain A residue  598 ILE
Chi-restraints excluded: chain A residue  639 ILE
Chi-restraints excluded: chain A residue  640 THR
Chi-restraints excluded: chain A residue  646 ILE
Chi-restraints excluded: chain A residue  750 ILE
Chi-restraints excluded: chain A residue  833 ASN
Chi-restraints excluded: chain A residue  845 LEU
Chi-restraints excluded: chain B residue   36 ILE
Chi-restraints excluded: chain B residue   79 VAL
Chi-restraints excluded: chain B residue  132 VAL
Chi-restraints excluded: chain B residue  221 ASN
Chi-restraints excluded: chain B residue  315 LEU
Chi-restraints excluded: chain B residue  372 ILE
Chi-restraints excluded: chain B residue  375 LYS
Chi-restraints excluded: chain B residue  470 THR
Chi-restraints excluded: chain B residue  544 HIS
Chi-restraints excluded: chain B residue  598 ILE
Chi-restraints excluded: chain B residue  639 ILE
Chi-restraints excluded: chain B residue  640 THR
Chi-restraints excluded: chain B residue  650 VAL
Chi-restraints excluded: chain B residue  750 ILE
Chi-restraints excluded: chain B residue  813 THR
Chi-restraints excluded: chain B residue  826 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 11 optimal weight:    4.9990
   chunk 149 optimal weight:    6.9990
   chunk 83 optimal weight:    5.9990
   chunk 119 optimal weight:    2.9990
   chunk 137 optimal weight:    0.6980
   chunk 52 optimal weight:    0.1980
   chunk 74 optimal weight:    0.9990
   chunk 34 optimal weight:    1.9990
   chunk 124 optimal weight:    3.9990
   chunk 55 optimal weight:    5.9990
   chunk 50 optimal weight:    0.9990
   overall best weight:    0.9786

-------------------------------------------------------------------------------
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 = 0.4118 r_free = 0.4118 target = 0.172862 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3785 r_free = 0.3785 target = 0.143185 restraints weight = 20158.159|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3764 r_free = 0.3764 target = 0.141828 restraints weight = 14104.648|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3767 r_free = 0.3767 target = 0.142515 restraints weight = 16037.875|
|-----------------------------------------------------------------------------|
r_work (final): 0.3764
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7304
moved from start:          0.3771

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.043  12320  Z= 0.111
  Angle     :  0.513   9.779  16704  Z= 0.267
  Chirality :  0.042   0.159   1894
  Planarity :  0.004   0.046   2158
  Dihedral  :  5.064  57.774   1658
  Min Nonbonded Distance : 2.574

Molprobity Statistics.
  All-atom Clashscore : 6.62
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  3.10 %
    Favored  : 96.83 %
  Rotamer:
    Outliers :  2.73 %
    Allowed  : 19.42 %
    Favored  : 77.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.82 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.15 (0.22), residues: 1514
  helix:  1.88 (0.19), residues: 766
  sheet:  0.20 (0.40), residues: 182
  loop : -0.56 (0.26), residues: 566

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B  43 
 HIS   0.003   0.001   HIS B 264 
 PHE   0.013   0.001   PHE B 668 
 TYR   0.015   0.001   TYR A 188 
 ARG   0.005   0.000   ARG A 796 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03920 (  669)
  hydrogen bonds       : angle       4.00087 ( 2058)
  covalent geometry    : bond        0.00245 (12320)
  covalent geometry    : angle       0.51270 (16704)

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

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

  3028 Ramachandran restraints generated.
    1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3028 Ramachandran restraints generated.
    1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 137
  time to evaluate  : 1.320 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  125 LEU cc_start: 0.8170 (OUTLIER) cc_final: 0.7785 (mp)
REVERT: A  253 LEU cc_start: 0.6312 (mt) cc_final: 0.6052 (mt)
REVERT: A  639 ILE cc_start: 0.8024 (OUTLIER) cc_final: 0.7750 (mp)
REVERT: A  668 PHE cc_start: 0.7523 (t80) cc_final: 0.7071 (t80)
REVERT: A  672 MET cc_start: 0.6782 (ttm) cc_final: 0.6531 (tmm)
REVERT: B  253 LEU cc_start: 0.6515 (mt) cc_final: 0.6254 (mt)
REVERT: B  639 ILE cc_start: 0.7848 (OUTLIER) cc_final: 0.7596 (mp)
REVERT: B  672 MET cc_start: 0.7342 (tmm) cc_final: 0.6718 (tmm)
REVERT: B  697 MET cc_start: 0.6531 (mtp) cc_final: 0.6326 (mtp)
REVERT: B  744 PHE cc_start: 0.7405 (m-80) cc_final: 0.7001 (m-80)
  outliers start: 36
  outliers final: 29
  residues processed: 167
  average time/residue: 0.2224
  time to fit residues: 55.0195
Evaluate side-chains
  160 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 128
  time to evaluate  : 1.382 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 ILE
Chi-restraints excluded: chain A residue   53 CYS
Chi-restraints excluded: chain A residue   79 VAL
Chi-restraints excluded: chain A residue  117 SER
Chi-restraints excluded: chain A residue  125 LEU
Chi-restraints excluded: chain A residue  132 VAL
Chi-restraints excluded: chain A residue  185 GLU
Chi-restraints excluded: chain A residue  221 ASN
Chi-restraints excluded: chain A residue  315 LEU
Chi-restraints excluded: chain A residue  375 LYS
Chi-restraints excluded: chain A residue  388 THR
Chi-restraints excluded: chain A residue  470 THR
Chi-restraints excluded: chain A residue  544 HIS
Chi-restraints excluded: chain A residue  598 ILE
Chi-restraints excluded: chain A residue  639 ILE
Chi-restraints excluded: chain A residue  640 THR
Chi-restraints excluded: chain A residue  750 ILE
Chi-restraints excluded: chain A residue  845 LEU
Chi-restraints excluded: chain B residue   79 VAL
Chi-restraints excluded: chain B residue  132 VAL
Chi-restraints excluded: chain B residue  315 LEU
Chi-restraints excluded: chain B residue  375 LYS
Chi-restraints excluded: chain B residue  470 THR
Chi-restraints excluded: chain B residue  544 HIS
Chi-restraints excluded: chain B residue  553 ILE
Chi-restraints excluded: chain B residue  598 ILE
Chi-restraints excluded: chain B residue  615 THR
Chi-restraints excluded: chain B residue  639 ILE
Chi-restraints excluded: chain B residue  650 VAL
Chi-restraints excluded: chain B residue  750 ILE
Chi-restraints excluded: chain B residue  813 THR
Chi-restraints excluded: chain B residue  826 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 47 optimal weight:    0.6980
   chunk 124 optimal weight:    7.9990
   chunk 108 optimal weight:    6.9990
   chunk 64 optimal weight:   10.0000
   chunk 20 optimal weight:    5.9990
   chunk 59 optimal weight:    5.9990
   chunk 14 optimal weight:    0.9980
   chunk 36 optimal weight:    1.9990
   chunk 55 optimal weight:    4.9990
   chunk 123 optimal weight:    1.9990
   chunk 147 optimal weight:   10.0000
   overall best weight:    2.1386

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

Flipped N/Q/H residues before XYZ refinement:
A 621 GLN
A 809 GLN
A 833 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4076 r_free = 0.4076 target = 0.169057 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3732 r_free = 0.3732 target = 0.139022 restraints weight = 20139.347|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3717 r_free = 0.3717 target = 0.138166 restraints weight = 14730.786|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3718 r_free = 0.3718 target = 0.138751 restraints weight = 15612.252|
|-----------------------------------------------------------------------------|
r_work (final): 0.3717
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7389
moved from start:          0.3836

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047  12320  Z= 0.164
  Angle     :  0.574   8.768  16704  Z= 0.303
  Chirality :  0.044   0.218   1894
  Planarity :  0.005   0.058   2158
  Dihedral  :  5.139  59.386   1655
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 6.67
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  3.90 %
    Favored  : 96.04 %
  Rotamer:
    Outliers :  3.41 %
    Allowed  : 19.65 %
    Favored  : 76.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.82 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.97 (0.22), residues: 1514
  helix:  1.79 (0.19), residues: 756
  sheet:  0.02 (0.39), residues: 196
  loop : -0.67 (0.26), residues: 562

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B  43 
 HIS   0.005   0.001   HIS B 264 
 PHE   0.013   0.001   PHE B 502 
 TYR   0.022   0.002   TYR B 188 
 ARG   0.005   0.000   ARG A 796 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04985 (  669)
  hydrogen bonds       : angle       4.25524 ( 2058)
  covalent geometry    : bond        0.00377 (12320)
  covalent geometry    : angle       0.57402 (16704)

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

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

  3028 Ramachandran restraints generated.
    1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3028 Ramachandran restraints generated.
    1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  177 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 132
  time to evaluate  : 1.469 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  125 LEU cc_start: 0.8193 (OUTLIER) cc_final: 0.7836 (mp)
REVERT: A  576 ASP cc_start: 0.5941 (m-30) cc_final: 0.5741 (m-30)
REVERT: A  639 ILE cc_start: 0.7981 (OUTLIER) cc_final: 0.7704 (mp)
REVERT: A  668 PHE cc_start: 0.7581 (t80) cc_final: 0.7197 (t80)
REVERT: A  672 MET cc_start: 0.7048 (ttm) cc_final: 0.6680 (tmm)
REVERT: B  253 LEU cc_start: 0.6718 (mt) cc_final: 0.6452 (mt)
REVERT: B  639 ILE cc_start: 0.7997 (OUTLIER) cc_final: 0.7741 (mp)
REVERT: B  672 MET cc_start: 0.7434 (tmm) cc_final: 0.6800 (tmm)
  outliers start: 45
  outliers final: 36
  residues processed: 172
  average time/residue: 0.2905
  time to fit residues: 74.7744
Evaluate side-chains
  163 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 124
  time to evaluate  : 1.366 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 ILE
Chi-restraints excluded: chain A residue   53 CYS
Chi-restraints excluded: chain A residue   79 VAL
Chi-restraints excluded: chain A residue  117 SER
Chi-restraints excluded: chain A residue  125 LEU
Chi-restraints excluded: chain A residue  132 VAL
Chi-restraints excluded: chain A residue  161 ASP
Chi-restraints excluded: chain A residue  185 GLU
Chi-restraints excluded: chain A residue  259 ILE
Chi-restraints excluded: chain A residue  315 LEU
Chi-restraints excluded: chain A residue  372 ILE
Chi-restraints excluded: chain A residue  375 LYS
Chi-restraints excluded: chain A residue  388 THR
Chi-restraints excluded: chain A residue  470 THR
Chi-restraints excluded: chain A residue  544 HIS
Chi-restraints excluded: chain A residue  598 ILE
Chi-restraints excluded: chain A residue  639 ILE
Chi-restraints excluded: chain A residue  750 ILE
Chi-restraints excluded: chain A residue  833 ASN
Chi-restraints excluded: chain A residue  845 LEU
Chi-restraints excluded: chain B residue   36 ILE
Chi-restraints excluded: chain B residue   79 VAL
Chi-restraints excluded: chain B residue  117 SER
Chi-restraints excluded: chain B residue  132 VAL
Chi-restraints excluded: chain B residue  259 ILE
Chi-restraints excluded: chain B residue  315 LEU
Chi-restraints excluded: chain B residue  372 ILE
Chi-restraints excluded: chain B residue  375 LYS
Chi-restraints excluded: chain B residue  470 THR
Chi-restraints excluded: chain B residue  544 HIS
Chi-restraints excluded: chain B residue  553 ILE
Chi-restraints excluded: chain B residue  598 ILE
Chi-restraints excluded: chain B residue  615 THR
Chi-restraints excluded: chain B residue  639 ILE
Chi-restraints excluded: chain B residue  640 THR
Chi-restraints excluded: chain B residue  650 VAL
Chi-restraints excluded: chain B residue  750 ILE
Chi-restraints excluded: chain B residue  813 THR
Chi-restraints excluded: chain B residue  826 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 84 optimal weight:    0.0970
   chunk 142 optimal weight:    5.9990
   chunk 100 optimal weight:    2.9990
   chunk 12 optimal weight:    0.5980
   chunk 138 optimal weight:    2.9990
   chunk 11 optimal weight:    4.9990
   chunk 89 optimal weight:    5.9990
   chunk 83 optimal weight:    4.9990
   chunk 60 optimal weight:    5.9990
   chunk 31 optimal weight:    4.9990
   chunk 1 optimal weight:    5.9990
   overall best weight:    2.3384

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

Flipped N/Q/H residues before XYZ refinement:
A 754 HIS
A 833 ASN
** B 833 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4065 r_free = 0.4065 target = 0.168370 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3742 r_free = 0.3742 target = 0.139633 restraints weight = 20126.628|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3718 r_free = 0.3718 target = 0.138379 restraints weight = 15652.619|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3723 r_free = 0.3723 target = 0.139368 restraints weight = 15389.609|
|-----------------------------------------------------------------------------|
r_work (final): 0.3721
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7379
moved from start:          0.3983

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047  12320  Z= 0.173
  Angle     :  0.584  12.178  16704  Z= 0.306
  Chirality :  0.045   0.207   1894
  Planarity :  0.005   0.044   2158
  Dihedral  :  5.162  59.718   1654
  Min Nonbonded Distance : 2.573

Molprobity Statistics.
  All-atom Clashscore : 6.42
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  3.76 %
    Favored  : 96.17 %
  Rotamer:
    Outliers :  3.41 %
    Allowed  : 20.11 %
    Favored  : 76.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.82 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.81 (0.22), residues: 1514
  helix:  1.66 (0.19), residues: 756
  sheet:  0.02 (0.40), residues: 182
  loop : -0.79 (0.26), residues: 576

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B  43 
 HIS   0.004   0.001   HIS B 264 
 PHE   0.033   0.002   PHE A 770 
 TYR   0.021   0.002   TYR B 188 
 ARG   0.004   0.000   ARG B 796 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05035 (  669)
  hydrogen bonds       : angle       4.33842 ( 2058)
  covalent geometry    : bond        0.00403 (12320)
  covalent geometry    : angle       0.58389 (16704)

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

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

  3028 Ramachandran restraints generated.
    1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3028 Ramachandran restraints generated.
    1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  174 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 129
  time to evaluate  : 1.531 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  125 LEU cc_start: 0.8201 (OUTLIER) cc_final: 0.7805 (mp)
REVERT: A  639 ILE cc_start: 0.7971 (OUTLIER) cc_final: 0.7715 (mp)
REVERT: A  668 PHE cc_start: 0.7566 (t80) cc_final: 0.7192 (t80)
REVERT: A  672 MET cc_start: 0.7036 (ttm) cc_final: 0.6627 (tmm)
REVERT: B  639 ILE cc_start: 0.8025 (OUTLIER) cc_final: 0.7764 (mp)
REVERT: B  672 MET cc_start: 0.7466 (tmm) cc_final: 0.6782 (tmm)
REVERT: B  685 LEU cc_start: 0.7919 (tp) cc_final: 0.7683 (tp)
  outliers start: 45
  outliers final: 38
  residues processed: 165
  average time/residue: 0.2436
  time to fit residues: 58.8907
Evaluate side-chains
  161 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 120
  time to evaluate  : 1.396 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 ILE
Chi-restraints excluded: chain A residue   53 CYS
Chi-restraints excluded: chain A residue   79 VAL
Chi-restraints excluded: chain A residue  117 SER
Chi-restraints excluded: chain A residue  125 LEU
Chi-restraints excluded: chain A residue  132 VAL
Chi-restraints excluded: chain A residue  161 ASP
Chi-restraints excluded: chain A residue  185 GLU
Chi-restraints excluded: chain A residue  221 ASN
Chi-restraints excluded: chain A residue  315 LEU
Chi-restraints excluded: chain A residue  372 ILE
Chi-restraints excluded: chain A residue  388 THR
Chi-restraints excluded: chain A residue  470 THR
Chi-restraints excluded: chain A residue  544 HIS
Chi-restraints excluded: chain A residue  598 ILE
Chi-restraints excluded: chain A residue  639 ILE
Chi-restraints excluded: chain A residue  651 VAL
Chi-restraints excluded: chain A residue  741 VAL
Chi-restraints excluded: chain A residue  742 THR
Chi-restraints excluded: chain A residue  833 ASN
Chi-restraints excluded: chain A residue  845 LEU
Chi-restraints excluded: chain B residue   36 ILE
Chi-restraints excluded: chain B residue   79 VAL
Chi-restraints excluded: chain B residue  117 SER
Chi-restraints excluded: chain B residue  132 VAL
Chi-restraints excluded: chain B residue  185 GLU
Chi-restraints excluded: chain B residue  315 LEU
Chi-restraints excluded: chain B residue  372 ILE
Chi-restraints excluded: chain B residue  375 LYS
Chi-restraints excluded: chain B residue  470 THR
Chi-restraints excluded: chain B residue  544 HIS
Chi-restraints excluded: chain B residue  553 ILE
Chi-restraints excluded: chain B residue  598 ILE
Chi-restraints excluded: chain B residue  615 THR
Chi-restraints excluded: chain B residue  639 ILE
Chi-restraints excluded: chain B residue  640 THR
Chi-restraints excluded: chain B residue  650 VAL
Chi-restraints excluded: chain B residue  741 VAL
Chi-restraints excluded: chain B residue  812 SER
Chi-restraints excluded: chain B residue  813 THR
Chi-restraints excluded: chain B residue  826 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 33 optimal weight:    3.9990
   chunk 149 optimal weight:    6.9990
   chunk 4 optimal weight:    0.9980
   chunk 59 optimal weight:    4.9990
   chunk 54 optimal weight:    0.9990
   chunk 102 optimal weight:    4.9990
   chunk 77 optimal weight:    1.9990
   chunk 73 optimal weight:   20.0000
   chunk 67 optimal weight:    5.9990
   chunk 30 optimal weight:    4.9990
   chunk 26 optimal weight:    7.9990
   overall best weight:    2.5988

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

Flipped N/Q/H residues before XYZ refinement:
A 833 ASN
B 505 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4055 r_free = 0.4055 target = 0.167393 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3720 r_free = 0.3720 target = 0.138116 restraints weight = 19986.798|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3706 r_free = 0.3706 target = 0.137345 restraints weight = 14492.213|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3700 r_free = 0.3700 target = 0.137507 restraints weight = 16901.668|
|-----------------------------------------------------------------------------|
r_work (final): 0.3700
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7419
moved from start:          0.4130

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047  12320  Z= 0.187
  Angle     :  0.614   8.689  16704  Z= 0.323
  Chirality :  0.046   0.228   1894
  Planarity :  0.005   0.045   2158
  Dihedral  :  5.142  59.890   1652
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 6.87
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  4.43 %
    Favored  : 95.51 %
  Rotamer:
    Outliers :  3.79 %
    Allowed  : 19.88 %
    Favored  : 76.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.82 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.67 (0.22), residues: 1514
  helix:  1.54 (0.19), residues: 758
  sheet: -0.02 (0.39), residues: 188
  loop : -0.86 (0.26), residues: 568

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B  43 
 HIS   0.004   0.001   HIS B 264 
 PHE   0.022   0.002   PHE A 770 
 TYR   0.022   0.002   TYR B 188 
 ARG   0.004   0.000   ARG B 753 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05331 (  669)
  hydrogen bonds       : angle       4.40063 ( 2058)
  covalent geometry    : bond        0.00437 (12320)
  covalent geometry    : angle       0.61427 (16704)

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

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

  3028 Ramachandran restraints generated.
    1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3028 Ramachandran restraints generated.
    1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 123
  time to evaluate  : 1.842 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  125 LEU cc_start: 0.8197 (OUTLIER) cc_final: 0.7808 (mp)
REVERT: A  639 ILE cc_start: 0.8034 (OUTLIER) cc_final: 0.7809 (mp)
REVERT: A  668 PHE cc_start: 0.7573 (t80) cc_final: 0.7199 (t80)
REVERT: A  672 MET cc_start: 0.7125 (ttm) cc_final: 0.6707 (tmm)
REVERT: B  639 ILE cc_start: 0.8006 (OUTLIER) cc_final: 0.7728 (mp)
REVERT: B  672 MET cc_start: 0.7461 (tmm) cc_final: 0.6805 (tmm)
REVERT: B  685 LEU cc_start: 0.7998 (tp) cc_final: 0.7746 (tp)
REVERT: B  796 ARG cc_start: 0.7124 (mpp80) cc_final: 0.6731 (mpp80)
  outliers start: 50
  outliers final: 42
  residues processed: 165
  average time/residue: 0.2584
  time to fit residues: 62.9397
Evaluate side-chains
  164 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 119
  time to evaluate  : 2.103 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 ILE
Chi-restraints excluded: chain A residue   53 CYS
Chi-restraints excluded: chain A residue   79 VAL
Chi-restraints excluded: chain A residue  117 SER
Chi-restraints excluded: chain A residue  125 LEU
Chi-restraints excluded: chain A residue  132 VAL
Chi-restraints excluded: chain A residue  161 ASP
Chi-restraints excluded: chain A residue  185 GLU
Chi-restraints excluded: chain A residue  221 ASN
Chi-restraints excluded: chain A residue  259 ILE
Chi-restraints excluded: chain A residue  315 LEU
Chi-restraints excluded: chain A residue  372 ILE
Chi-restraints excluded: chain A residue  388 THR
Chi-restraints excluded: chain A residue  470 THR
Chi-restraints excluded: chain A residue  544 HIS
Chi-restraints excluded: chain A residue  598 ILE
Chi-restraints excluded: chain A residue  639 ILE
Chi-restraints excluded: chain A residue  651 VAL
Chi-restraints excluded: chain A residue  689 LEU
Chi-restraints excluded: chain A residue  741 VAL
Chi-restraints excluded: chain A residue  742 THR
Chi-restraints excluded: chain A residue  833 ASN
Chi-restraints excluded: chain A residue  845 LEU
Chi-restraints excluded: chain B residue   36 ILE
Chi-restraints excluded: chain B residue   79 VAL
Chi-restraints excluded: chain B residue  117 SER
Chi-restraints excluded: chain B residue  132 VAL
Chi-restraints excluded: chain B residue  185 GLU
Chi-restraints excluded: chain B residue  200 VAL
Chi-restraints excluded: chain B residue  259 ILE
Chi-restraints excluded: chain B residue  315 LEU
Chi-restraints excluded: chain B residue  372 ILE
Chi-restraints excluded: chain B residue  375 LYS
Chi-restraints excluded: chain B residue  470 THR
Chi-restraints excluded: chain B residue  544 HIS
Chi-restraints excluded: chain B residue  553 ILE
Chi-restraints excluded: chain B residue  598 ILE
Chi-restraints excluded: chain B residue  615 THR
Chi-restraints excluded: chain B residue  639 ILE
Chi-restraints excluded: chain B residue  640 THR
Chi-restraints excluded: chain B residue  650 VAL
Chi-restraints excluded: chain B residue  741 VAL
Chi-restraints excluded: chain B residue  812 SER
Chi-restraints excluded: chain B residue  813 THR
Chi-restraints excluded: chain B residue  826 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 87 optimal weight:    1.9990
   chunk 149 optimal weight:    6.9990
   chunk 115 optimal weight:    4.9990
   chunk 98 optimal weight:    0.9990
   chunk 27 optimal weight:    0.9990
   chunk 75 optimal weight:    3.9990
   chunk 139 optimal weight:    0.9990
   chunk 45 optimal weight:    3.9990
   chunk 29 optimal weight:    0.0010
   chunk 110 optimal weight:    6.9990
   chunk 12 optimal weight:    0.8980
   overall best weight:    0.7792

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

Flipped N/Q/H residues before XYZ refinement:
A 833 ASN
B 833 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4099 r_free = 0.4099 target = 0.171447 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3778 r_free = 0.3778 target = 0.142578 restraints weight = 19938.371|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3754 r_free = 0.3754 target = 0.140838 restraints weight = 14775.045|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3758 r_free = 0.3758 target = 0.141770 restraints weight = 16147.640|
|-----------------------------------------------------------------------------|
r_work (final): 0.3754
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7320
moved from start:          0.4363

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.043  12320  Z= 0.110
  Angle     :  0.544   8.970  16704  Z= 0.281
  Chirality :  0.043   0.248   1894
  Planarity :  0.004   0.042   2158
  Dihedral  :  4.894  59.970   1652
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 5.96
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  2.77 %
    Favored  : 97.16 %
  Rotamer:
    Outliers :  2.20 %
    Allowed  : 21.47 %
    Favored  : 76.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.82 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.99 (0.22), residues: 1514
  helix:  1.81 (0.19), residues: 762
  sheet:  0.19 (0.41), residues: 182
  loop : -0.75 (0.26), residues: 570

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B  43 
 HIS   0.002   0.000   HIS B 103 
 PHE   0.022   0.001   PHE A 770 
 TYR   0.012   0.001   TYR B 188 
 ARG   0.004   0.000   ARG B 753 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03883 (  669)
  hydrogen bonds       : angle       4.08620 ( 2058)
  covalent geometry    : bond        0.00235 (12320)
  covalent geometry    : angle       0.54437 (16704)

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

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

  3028 Ramachandran restraints generated.
    1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3028 Ramachandran restraints generated.
    1514 Oldfield, 0 Emsley, 1514 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 133
  time to evaluate  : 1.957 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  253 LEU cc_start: 0.6498 (mt) cc_final: 0.6240 (mt)
REVERT: A  486 MET cc_start: 0.8229 (ptm) cc_final: 0.7814 (ptt)
REVERT: A  639 ILE cc_start: 0.7916 (OUTLIER) cc_final: 0.7659 (mp)
REVERT: A  668 PHE cc_start: 0.7539 (t80) cc_final: 0.7169 (t80)
REVERT: A  672 MET cc_start: 0.7024 (ttm) cc_final: 0.6547 (tmm)
REVERT: B  639 ILE cc_start: 0.7956 (OUTLIER) cc_final: 0.7701 (mp)
REVERT: B  672 MET cc_start: 0.7390 (tmm) cc_final: 0.6732 (tmm)
REVERT: B  685 LEU cc_start: 0.7862 (tp) cc_final: 0.7539 (tp)
  outliers start: 29
  outliers final: 23
  residues processed: 160
  average time/residue: 0.2828
  time to fit residues: 67.1877
Evaluate side-chains
  149 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 124
  time to evaluate  : 1.306 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   79 VAL
Chi-restraints excluded: chain A residue  117 SER
Chi-restraints excluded: chain A residue  132 VAL
Chi-restraints excluded: chain A residue  315 LEU
Chi-restraints excluded: chain A residue  388 THR
Chi-restraints excluded: chain A residue  544 HIS
Chi-restraints excluded: chain A residue  598 ILE
Chi-restraints excluded: chain A residue  639 ILE
Chi-restraints excluded: chain A residue  742 THR
Chi-restraints excluded: chain A residue  833 ASN
Chi-restraints excluded: chain A residue  845 LEU
Chi-restraints excluded: chain B residue   79 VAL
Chi-restraints excluded: chain B residue  117 SER
Chi-restraints excluded: chain B residue  132 VAL
Chi-restraints excluded: chain B residue  200 VAL
Chi-restraints excluded: chain B residue  544 HIS
Chi-restraints excluded: chain B residue  553 ILE
Chi-restraints excluded: chain B residue  598 ILE
Chi-restraints excluded: chain B residue  615 THR
Chi-restraints excluded: chain B residue  639 ILE
Chi-restraints excluded: chain B residue  640 THR
Chi-restraints excluded: chain B residue  741 VAL
Chi-restraints excluded: chain B residue  812 SER
Chi-restraints excluded: chain B residue  813 THR
Chi-restraints excluded: chain B residue  826 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 99 optimal weight:    2.9990
   chunk 118 optimal weight:    0.9980
   chunk 87 optimal weight:    1.9990
   chunk 95 optimal weight:    6.9990
   chunk 77 optimal weight:    2.9990
   chunk 28 optimal weight:    0.9990
   chunk 23 optimal weight:    3.9990
   chunk 32 optimal weight:    5.9990
   chunk 110 optimal weight:    7.9990
   chunk 12 optimal weight:    0.2980
   chunk 14 optimal weight:    0.9980
   overall best weight:    1.0584

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

Flipped N/Q/H residues before XYZ refinement:
A 833 ASN
B 621 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4096 r_free = 0.4096 target = 0.171046 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3762 r_free = 0.3762 target = 0.141474 restraints weight = 20134.876|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3740 r_free = 0.3740 target = 0.140427 restraints weight = 14458.884|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3741 r_free = 0.3741 target = 0.140995 restraints weight = 15898.960|
|-----------------------------------------------------------------------------|
r_work (final): 0.3730
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7347
moved from start:          0.4454

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  12320  Z= 0.117
  Angle     :  0.555  10.920  16704  Z= 0.285
  Chirality :  0.043   0.205   1894
  Planarity :  0.005   0.043   2158
  Dihedral  :  4.841  58.665   1652
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 6.21
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  3.30 %
    Favored  : 96.63 %
  Rotamer:
    Outliers :  2.05 %
    Allowed  : 21.93 %
    Favored  : 76.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.82 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.98 (0.22), residues: 1514
  helix:  1.77 (0.19), residues: 778
  sheet:  0.24 (0.41), residues: 182
  loop : -0.81 (0.26), residues: 554

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B  43 
 HIS   0.003   0.001   HIS B 264 
 PHE   0.020   0.001   PHE A 770 
 TYR   0.015   0.001   TYR B 188 
 ARG   0.006   0.000   ARG A 703 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03988 (  669)
  hydrogen bonds       : angle       4.03170 ( 2058)
  covalent geometry    : bond        0.00258 (12320)
  covalent geometry    : angle       0.55492 (16704)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3872.61 seconds
wall clock time: 70 minutes 51.69 seconds (4251.69 seconds total)