Starting phenix.real_space_refine
on Sat May 17 18:45:45 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7yea_33768/05_2025/7yea_33768.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7yea_33768/05_2025/7yea_33768.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.82
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7yea_33768/05_2025/7yea_33768.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7yea_33768/05_2025/7yea_33768.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7yea_33768/05_2025/7yea_33768.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7yea_33768/05_2025/7yea_33768.cif"
  }
  resolution = 3.82
  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=  -0.000 sd=   0.043
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     100      5.16       5
     C   10146      2.51       5
     N    2810      2.21       5
     O    2960      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 27 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 16016
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 8008
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1017, 8008
          Classifications: {'peptide': 1017}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 52, 'TRANS': 963}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 1
          Unresolved non-hydrogen dihedrals: 1
    Chain: "B"
      Number of atoms: 8008
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1017, 8008
          Classifications: {'peptide': 1017}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 52, 'TRANS': 963}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 1
          Unresolved non-hydrogen dihedrals: 1
  Time building chain proxies: 9.31, per 1000 atoms: 0.58
  Number of scatterers: 16016
  At special positions: 0
  Unit cell: (198.891, 109.347, 128.289, 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     100     16.00
     O    2960      8.00
     N    2810      7.00
     C   10146      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 4.03
  Conformation dependent library (CDL) restraints added in 2.0 seconds
  

  4060 Ramachandran restraints generated.
    2030 Oldfield, 0 Emsley, 2030 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3844

  Finding SS restraints...
    Secondary structure from input PDB file:
      108 helices and 8 sheets defined
      65.5% alpha, 5.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.93
  Creating SS restraints...
    Processing helix  chain 'A' and resid 26 through 35
    Processing helix  chain 'A' and resid 37 through 51
    Processing helix  chain 'A' and resid 55 through 68
    Processing helix  chain 'A' and resid 70 through 85
    Processing helix  chain 'A' and resid 88 through 103
      removed outlier: 4.120A  pdb=" N   TYR A  92 " --> pdb=" O   LEU A  88 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 104 through 115
    Processing helix  chain 'A' and resid 123 through 135
      removed outlier: 3.528A  pdb=" N   ILE A 127 " --> pdb=" O   ILE A 123 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 138 through 153
    Processing helix  chain 'A' and resid 159 through 171
      removed outlier: 3.759A  pdb=" N   ALA A 169 " --> pdb=" O   ASN A 165 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 172 through 187
      removed outlier: 4.496A  pdb=" N   ALA A 178 " --> pdb=" O   GLU A 174 " (cutoff:3.500A)
      removed outlier: 4.317A  pdb=" N   CYS A 179 " --> pdb=" O   GLU A 175 " (cutoff:3.500A)
      removed outlier: 3.582A  pdb=" N   TYR A 180 " --> pdb=" O   ALA A 176 " (cutoff:3.500A)
      removed outlier: 3.939A  pdb=" N   LEU A 181 " --> pdb=" O   LYS A 177 " (cutoff:3.500A)
      removed outlier: 4.021A  pdb=" N   LYS A 182 " --> pdb=" O   ALA A 178 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 194 through 205
    Processing helix  chain 'A' and resid 206 through 220
      removed outlier: 3.556A  pdb=" N   ALA A 210 " --> pdb=" O   GLU A 206 " (cutoff:3.500A)
      removed outlier: 4.114A  pdb=" N   HIS A 212 " --> pdb=" O   TRP A 208 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 225 through 238
      removed outlier: 3.714A  pdb=" N   ALA A 238 " --> pdb=" O   VAL A 234 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 241 through 253
    Processing helix  chain 'A' and resid 260 through 273
      removed outlier: 3.528A  pdb=" N   ASN A 264 " --> pdb=" O   VAL A 260 " (cutoff:3.500A)
      removed outlier: 3.801A  pdb=" N   ALA A 266 " --> pdb=" O   HIS A 262 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 274 through 289
    Processing helix  chain 'A' and resid 292 through 305
      removed outlier: 3.506A  pdb=" N   TYR A 296 " --> pdb=" O   PHE A 292 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 308 through 323
    Processing helix  chain 'A' and resid 326 through 339
    Processing helix  chain 'A' and resid 342 through 357
    Processing helix  chain 'A' and resid 360 through 375
    Processing helix  chain 'A' and resid 377 through 391
    Processing helix  chain 'A' and resid 394 through 409
      removed outlier: 3.588A  pdb=" N   TYR A 398 " --> pdb=" O   PHE A 394 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 411 through 425
      removed outlier: 3.573A  pdb=" N   LEU A 415 " --> pdb=" O   VAL A 411 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 428 through 443
    Processing helix  chain 'A' and resid 444 through 459
    Processing helix  chain 'A' and resid 462 through 476
      removed outlier: 3.661A  pdb=" N   TYR A 466 " --> pdb=" O   PHE A 462 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 481 through 499
    Processing helix  chain 'A' and resid 507 through 513
      removed outlier: 3.741A  pdb=" N   MET A 511 " --> pdb=" O   HIS A 508 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 516 through 538
      removed outlier: 3.870A  pdb=" N   VAL A 537 " --> pdb=" O   ASP A 533 " (cutoff:3.500A)
      removed outlier: 4.316A  pdb=" N   LEU A 538 " --> pdb=" O   LYS A 534 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 570 through 575
    Processing helix  chain 'A' and resid 576 through 581
      removed outlier: 3.538A  pdb=" N   MET A 580 " --> pdb=" O   ILE A 577 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 599 through 608
    Processing helix  chain 'A' and resid 620 through 632
      removed outlier: 3.503A  pdb=" N   ALA A 624 " --> pdb=" O   CYS A 620 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 648 through 653
    Processing helix  chain 'A' and resid 685 through 692
      removed outlier: 4.263A  pdb=" N   GLU A 690 " --> pdb=" O   GLU A 687 " (cutoff:3.500A)
      removed outlier: 3.892A  pdb=" N   TYR A 692 " --> pdb=" O   ALA A 689 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 707 through 712
      removed outlier: 3.752A  pdb=" N   MET A 711 " --> pdb=" O   ASP A 707 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 713 through 717
      removed outlier: 3.765A  pdb=" N   LYS A 717 " --> pdb=" O   HIS A 714 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 740 through 746
      removed outlier: 3.816A  pdb=" N   ASP A 746 " --> pdb=" O   LYS A 742 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 780 through 792
      removed outlier: 3.643A  pdb=" N   ARG A 792 " --> pdb=" O   GLU A 788 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 809 through 814
    Processing helix  chain 'A' and resid 814 through 819
      removed outlier: 3.823A  pdb=" N   ALA A 818 " --> pdb=" O   ASN A 814 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 833 through 836
    Processing helix  chain 'A' and resid 854 through 867
    Processing helix  chain 'A' and resid 879 through 881
      No H-bonds generated for 'chain 'A' and resid 879 through 881'
    Processing helix  chain 'A' and resid 882 through 893
    Processing helix  chain 'A' and resid 907 through 914
    Processing helix  chain 'A' and resid 915 through 918
    Processing helix  chain 'A' and resid 931 through 940
    Processing helix  chain 'A' and resid 950 through 964
      removed outlier: 4.686A  pdb=" N   ALA A 956 " --> pdb=" O   ALA A 952 " (cutoff:3.500A)
      removed outlier: 5.290A  pdb=" N   ALA A 957 " --> pdb=" O   SER A 953 " (cutoff:3.500A)
      removed outlier: 3.954A  pdb=" N   SER A 958 " --> pdb=" O   ARG A 954 " (cutoff:3.500A)
      removed outlier: 3.941A  pdb=" N   GLN A 959 " --> pdb=" O   VAL A 955 " (cutoff:3.500A)
      removed outlier: 3.891A  pdb=" N   LEU A 960 " --> pdb=" O   ALA A 956 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 965 through 969
    Processing helix  chain 'A' and resid 972 through 986
    Processing helix  chain 'A' and resid 986 through 1004
      removed outlier: 3.754A  pdb=" N   ILE A1002 " --> pdb=" O   TRP A 998 " (cutoff:3.500A)
      removed outlier: 3.761A  pdb=" N   SER A1003 " --> pdb=" O   LYS A 999 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1008 through 1029
      removed outlier: 3.553A  pdb=" N   ALA A1029 " --> pdb=" O   GLU A1025 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 26 through 35
    Processing helix  chain 'B' and resid 37 through 51
    Processing helix  chain 'B' and resid 55 through 68
    Processing helix  chain 'B' and resid 70 through 85
    Processing helix  chain 'B' and resid 88 through 103
      removed outlier: 4.119A  pdb=" N   TYR B  92 " --> pdb=" O   LEU B  88 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 104 through 115
    Processing helix  chain 'B' and resid 123 through 135
      removed outlier: 3.529A  pdb=" N   ILE B 127 " --> pdb=" O   ILE B 123 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 138 through 153
    Processing helix  chain 'B' and resid 159 through 171
      removed outlier: 3.758A  pdb=" N   ALA B 169 " --> pdb=" O   ASN B 165 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 172 through 187
      removed outlier: 4.496A  pdb=" N   ALA B 178 " --> pdb=" O   GLU B 174 " (cutoff:3.500A)
      removed outlier: 4.318A  pdb=" N   CYS B 179 " --> pdb=" O   GLU B 175 " (cutoff:3.500A)
      removed outlier: 3.582A  pdb=" N   TYR B 180 " --> pdb=" O   ALA B 176 " (cutoff:3.500A)
      removed outlier: 3.939A  pdb=" N   LEU B 181 " --> pdb=" O   LYS B 177 " (cutoff:3.500A)
      removed outlier: 4.021A  pdb=" N   LYS B 182 " --> pdb=" O   ALA B 178 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 194 through 205
    Processing helix  chain 'B' and resid 206 through 220
      removed outlier: 3.556A  pdb=" N   ALA B 210 " --> pdb=" O   GLU B 206 " (cutoff:3.500A)
      removed outlier: 4.114A  pdb=" N   HIS B 212 " --> pdb=" O   TRP B 208 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 225 through 238
      removed outlier: 3.714A  pdb=" N   ALA B 238 " --> pdb=" O   VAL B 234 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 241 through 253
    Processing helix  chain 'B' and resid 260 through 273
      removed outlier: 3.528A  pdb=" N   ASN B 264 " --> pdb=" O   VAL B 260 " (cutoff:3.500A)
      removed outlier: 3.801A  pdb=" N   ALA B 266 " --> pdb=" O   HIS B 262 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 274 through 289
    Processing helix  chain 'B' and resid 292 through 305
      removed outlier: 3.506A  pdb=" N   TYR B 296 " --> pdb=" O   PHE B 292 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 308 through 323
    Processing helix  chain 'B' and resid 326 through 339
    Processing helix  chain 'B' and resid 342 through 357
    Processing helix  chain 'B' and resid 360 through 375
    Processing helix  chain 'B' and resid 377 through 391
    Processing helix  chain 'B' and resid 394 through 409
      removed outlier: 3.587A  pdb=" N   TYR B 398 " --> pdb=" O   PHE B 394 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 411 through 425
      removed outlier: 3.573A  pdb=" N   LEU B 415 " --> pdb=" O   VAL B 411 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 428 through 443
    Processing helix  chain 'B' and resid 444 through 459
    Processing helix  chain 'B' and resid 462 through 476
      removed outlier: 3.661A  pdb=" N   TYR B 466 " --> pdb=" O   PHE B 462 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 481 through 499
    Processing helix  chain 'B' and resid 507 through 513
      removed outlier: 3.741A  pdb=" N   MET B 511 " --> pdb=" O   HIS B 508 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 516 through 538
      removed outlier: 3.869A  pdb=" N   VAL B 537 " --> pdb=" O   ASP B 533 " (cutoff:3.500A)
      removed outlier: 4.316A  pdb=" N   LEU B 538 " --> pdb=" O   LYS B 534 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 570 through 575
    Processing helix  chain 'B' and resid 576 through 581
      removed outlier: 3.539A  pdb=" N   MET B 580 " --> pdb=" O   ILE B 577 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 599 through 608
    Processing helix  chain 'B' and resid 620 through 632
      removed outlier: 3.504A  pdb=" N   ALA B 624 " --> pdb=" O   CYS B 620 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 648 through 653
    Processing helix  chain 'B' and resid 685 through 692
      removed outlier: 4.263A  pdb=" N   GLU B 690 " --> pdb=" O   GLU B 687 " (cutoff:3.500A)
      removed outlier: 3.893A  pdb=" N   TYR B 692 " --> pdb=" O   ALA B 689 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 707 through 712
      removed outlier: 3.752A  pdb=" N   MET B 711 " --> pdb=" O   ASP B 707 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 713 through 717
      removed outlier: 3.764A  pdb=" N   LYS B 717 " --> pdb=" O   HIS B 714 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 740 through 746
      removed outlier: 3.817A  pdb=" N   ASP B 746 " --> pdb=" O   LYS B 742 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 780 through 792
      removed outlier: 3.644A  pdb=" N   ARG B 792 " --> pdb=" O   GLU B 788 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 809 through 814
    Processing helix  chain 'B' and resid 814 through 819
      removed outlier: 3.823A  pdb=" N   ALA B 818 " --> pdb=" O   ASN B 814 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 833 through 836
    Processing helix  chain 'B' and resid 854 through 867
    Processing helix  chain 'B' and resid 879 through 881
      No H-bonds generated for 'chain 'B' and resid 879 through 881'
    Processing helix  chain 'B' and resid 882 through 893
    Processing helix  chain 'B' and resid 907 through 914
    Processing helix  chain 'B' and resid 915 through 918
    Processing helix  chain 'B' and resid 931 through 940
    Processing helix  chain 'B' and resid 950 through 964
      removed outlier: 4.686A  pdb=" N   ALA B 956 " --> pdb=" O   ALA B 952 " (cutoff:3.500A)
      removed outlier: 5.290A  pdb=" N   ALA B 957 " --> pdb=" O   SER B 953 " (cutoff:3.500A)
      removed outlier: 3.955A  pdb=" N   SER B 958 " --> pdb=" O   ARG B 954 " (cutoff:3.500A)
      removed outlier: 3.941A  pdb=" N   GLN B 959 " --> pdb=" O   VAL B 955 " (cutoff:3.500A)
      removed outlier: 3.892A  pdb=" N   LEU B 960 " --> pdb=" O   ALA B 956 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 965 through 969
    Processing helix  chain 'B' and resid 972 through 986
    Processing helix  chain 'B' and resid 986 through 1004
      removed outlier: 3.754A  pdb=" N   ILE B1002 " --> pdb=" O   TRP B 998 " (cutoff:3.500A)
      removed outlier: 3.761A  pdb=" N   SER B1003 " --> pdb=" O   LYS B 999 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1008 through 1029
      removed outlier: 3.553A  pdb=" N   ALA B1029 " --> pdb=" O   GLU B1025 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 612 through 614
      removed outlier: 6.231A  pdb=" N   LEU A 556 " --> pdb=" O   GLU A 587 " (cutoff:3.500A)
      removed outlier: 7.651A  pdb=" N   PHE A 589 " --> pdb=" O   LEU A 556 " (cutoff:3.500A)
      removed outlier: 6.421A  pdb=" N   VAL A 558 " --> pdb=" O   PHE A 589 " (cutoff:3.500A)
      removed outlier: 7.705A  pdb=" N   TYR A 591 " --> pdb=" O   VAL A 558 " (cutoff:3.500A)
      removed outlier: 6.464A  pdb=" N   TYR A 560 " --> pdb=" O   TYR A 591 " (cutoff:3.500A)
      removed outlier: 6.233A  pdb=" N   ARG A 557 " --> pdb=" O   ILE A 635 " (cutoff:3.500A)
      removed outlier: 7.691A  pdb=" N   VAL A 637 " --> pdb=" O   ARG A 557 " (cutoff:3.500A)
      removed outlier: 6.008A  pdb=" N   GLY A 559 " --> pdb=" O   VAL A 637 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 679 through 680
      removed outlier: 7.222A  pdb=" N   THR A 679 " --> pdb=" O   MET A 699 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'A' and resid 752 through 754
      removed outlier: 5.687A  pdb=" N   ILE A 734 " --> pdb=" O   ILE A 721 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 900 through 903
      removed outlier: 7.940A  pdb=" N   ILE A 901 " --> pdb=" O   SER A 871 " (cutoff:3.500A)
      removed outlier: 6.003A  pdb=" N   LEU A 873 " --> pdb=" O   ILE A 901 " (cutoff:3.500A)
      removed outlier: 7.656A  pdb=" N   SER A 903 " --> pdb=" O   LEU A 873 " (cutoff:3.500A)
      removed outlier: 6.828A  pdb=" N   LEU A 875 " --> pdb=" O   SER A 903 " (cutoff:3.500A)
      removed outlier: 5.823A  pdb=" N   ILE A 842 " --> pdb=" O   VAL A 872 " (cutoff:3.500A)
      removed outlier: 6.903A  pdb=" N   TRP A 874 " --> pdb=" O   ILE A 842 " (cutoff:3.500A)
      removed outlier: 6.736A  pdb=" N   TYR A 844 " --> pdb=" O   TRP A 874 " (cutoff:3.500A)
      removed outlier: 8.981A  pdb=" N   LEU A 876 " --> pdb=" O   TYR A 844 " (cutoff:3.500A)
      removed outlier: 6.057A  pdb=" N   VAL A 843 " --> pdb=" O   VAL A 920 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'B' and resid 612 through 614
      removed outlier: 6.229A  pdb=" N   LEU B 556 " --> pdb=" O   GLU B 587 " (cutoff:3.500A)
      removed outlier: 7.650A  pdb=" N   PHE B 589 " --> pdb=" O   LEU B 556 " (cutoff:3.500A)
      removed outlier: 6.421A  pdb=" N   VAL B 558 " --> pdb=" O   PHE B 589 " (cutoff:3.500A)
      removed outlier: 7.704A  pdb=" N   TYR B 591 " --> pdb=" O   VAL B 558 " (cutoff:3.500A)
      removed outlier: 6.463A  pdb=" N   TYR B 560 " --> pdb=" O   TYR B 591 " (cutoff:3.500A)
      removed outlier: 6.233A  pdb=" N   ARG B 557 " --> pdb=" O   ILE B 635 " (cutoff:3.500A)
      removed outlier: 7.691A  pdb=" N   VAL B 637 " --> pdb=" O   ARG B 557 " (cutoff:3.500A)
      removed outlier: 6.007A  pdb=" N   GLY B 559 " --> pdb=" O   VAL B 637 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 679 through 680
      removed outlier: 7.223A  pdb=" N   THR B 679 " --> pdb=" O   MET B 699 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'B' and resid 752 through 754
      removed outlier: 5.688A  pdb=" N   ILE B 734 " --> pdb=" O   ILE B 721 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 900 through 903
      removed outlier: 7.940A  pdb=" N   ILE B 901 " --> pdb=" O   SER B 871 " (cutoff:3.500A)
      removed outlier: 6.004A  pdb=" N   LEU B 873 " --> pdb=" O   ILE B 901 " (cutoff:3.500A)
      removed outlier: 7.656A  pdb=" N   SER B 903 " --> pdb=" O   LEU B 873 " (cutoff:3.500A)
      removed outlier: 6.827A  pdb=" N   LEU B 875 " --> pdb=" O   SER B 903 " (cutoff:3.500A)
      removed outlier: 5.824A  pdb=" N   ILE B 842 " --> pdb=" O   VAL B 872 " (cutoff:3.500A)
      removed outlier: 6.903A  pdb=" N   TRP B 874 " --> pdb=" O   ILE B 842 " (cutoff:3.500A)
      removed outlier: 6.735A  pdb=" N   TYR B 844 " --> pdb=" O   TRP B 874 " (cutoff:3.500A)
      removed outlier: 8.982A  pdb=" N   LEU B 876 " --> pdb=" O   TYR B 844 " (cutoff:3.500A)
      removed outlier: 6.057A  pdb=" N   VAL B 843 " --> pdb=" O   VAL B 920 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA8

    892 hydrogen bonds defined for protein.
    2568 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: 5.56

  Time building geometry restraints manager: 4.64 seconds

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

  Histogram of bond lengths:
        1.22 -     1.33: 5255
        1.33 -     1.45: 2369
        1.45 -     1.57: 8606
        1.57 -     1.69: 0
        1.69 -     1.81: 156
  Bond restraints: 16386
  Sorted by residual:
  bond pdb=" C   LEU A 512 "
       pdb=" N   TYR A 513 "
    ideal  model  delta    sigma   weight residual
    1.330  1.236  0.094 1.47e-02 4.63e+03 4.13e+01
  bond pdb=" C   LEU B 512 "
       pdb=" N   TYR B 513 "
    ideal  model  delta    sigma   weight residual
    1.330  1.236  0.094 1.47e-02 4.63e+03 4.11e+01
  bond pdb=" CB  TRP A 208 "
       pdb=" CG  TRP A 208 "
    ideal  model  delta    sigma   weight residual
    1.498  1.425  0.073 3.10e-02 1.04e+03 5.60e+00
  bond pdb=" CB  TRP B 208 "
       pdb=" CG  TRP B 208 "
    ideal  model  delta    sigma   weight residual
    1.498  1.425  0.073 3.10e-02 1.04e+03 5.57e+00
  bond pdb=" CB  LEU A 197 "
       pdb=" CG  LEU A 197 "
    ideal  model  delta    sigma   weight residual
    1.530  1.484  0.046 2.00e-02 2.50e+03 5.33e+00
  ... (remaining 16381 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.72: 21202
        1.72 -     3.45: 848
        3.45 -     5.17: 153
        5.17 -     6.90: 29
        6.90 -     8.62: 12
  Bond angle restraints: 22244
  Sorted by residual:
  angle pdb=" C   ALA A 217 "
        pdb=" N   VAL A 218 "
        pdb=" CA  VAL A 218 "
      ideal   model   delta    sigma   weight residual
     121.84  116.83    5.01 1.13e+00 7.83e-01 1.97e+01
  angle pdb=" C   ALA B 217 "
        pdb=" N   VAL B 218 "
        pdb=" CA  VAL B 218 "
      ideal   model   delta    sigma   weight residual
     121.84  116.84    5.00 1.13e+00 7.83e-01 1.96e+01
  angle pdb=" N   VAL B 218 "
        pdb=" CA  VAL B 218 "
        pdb=" C   VAL B 218 "
      ideal   model   delta    sigma   weight residual
     112.96  109.11    3.85 1.00e+00 1.00e+00 1.48e+01
  angle pdb=" N   VAL A 218 "
        pdb=" CA  VAL A 218 "
        pdb=" C   VAL A 218 "
      ideal   model   delta    sigma   weight residual
     112.96  109.15    3.81 1.00e+00 1.00e+00 1.45e+01
  angle pdb=" C   VAL A 605 "
        pdb=" N   MET A 606 "
        pdb=" CA  MET A 606 "
      ideal   model   delta    sigma   weight residual
     121.58  114.78    6.80 1.95e+00 2.63e-01 1.22e+01
  ... (remaining 22239 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.41: 8770
       16.41 -    32.83: 945
       32.83 -    49.24: 159
       49.24 -    65.66: 32
       65.66 -    82.07: 8
  Dihedral angle restraints: 9914
    sinusoidal: 3954
      harmonic: 5960
  Sorted by residual:
  dihedral pdb=" CA  ARG A 239 "
           pdb=" C   ARG A 239 "
           pdb=" N   ILE A 240 "
           pdb=" CA  ILE A 240 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  151.92   28.08     0      5.00e+00 4.00e-02 3.15e+01
  dihedral pdb=" CA  ARG B 239 "
           pdb=" C   ARG B 239 "
           pdb=" N   ILE B 240 "
           pdb=" CA  ILE B 240 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  151.95   28.05     0      5.00e+00 4.00e-02 3.15e+01
  dihedral pdb=" CA  HIS A 545 "
           pdb=" C   HIS A 545 "
           pdb=" N   PRO A 546 "
           pdb=" CA  PRO A 546 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -152.61  -27.39     0      5.00e+00 4.00e-02 3.00e+01
  ... (remaining 9911 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.042: 1604
       0.042 -    0.084: 621
       0.084 -    0.126: 192
       0.126 -    0.167: 19
       0.167 -    0.209: 6
  Chirality restraints: 2442
  Sorted by residual:
  chirality pdb=" CB  ILE A 795 "
            pdb=" CA  ILE A 795 "
            pdb=" CG1 ILE A 795 "
            pdb=" CG2 ILE A 795 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.44    0.21 2.00e-01 2.50e+01 1.09e+00
  chirality pdb=" CB  ILE B 795 "
            pdb=" CA  ILE B 795 "
            pdb=" CG1 ILE B 795 "
            pdb=" CG2 ILE B 795 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.44    0.21 2.00e-01 2.50e+01 1.07e+00
  chirality pdb=" CB  VAL A 218 "
            pdb=" CA  VAL A 218 "
            pdb=" CG1 VAL A 218 "
            pdb=" CG2 VAL A 218 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.44   -0.19 2.00e-01 2.50e+01 9.34e-01
  ... (remaining 2439 not shown)

  Planarity restraints: 2922
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 861 "   -0.027 2.00e-02 2.50e+03   2.67e-02 1.78e+01
        pdb=" CG  TRP A 861 "    0.073 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 861 "   -0.030 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 861 "    0.001 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 861 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 861 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 861 "   -0.013 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 861 "   -0.002 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 861 "   -0.002 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 861 "    0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP B 861 "   -0.027 2.00e-02 2.50e+03   2.65e-02 1.76e+01
        pdb=" CG  TRP B 861 "    0.072 2.00e-02 2.50e+03
        pdb=" CD1 TRP B 861 "   -0.030 2.00e-02 2.50e+03
        pdb=" CD2 TRP B 861 "    0.001 2.00e-02 2.50e+03
        pdb=" NE1 TRP B 861 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE2 TRP B 861 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE3 TRP B 861 "   -0.013 2.00e-02 2.50e+03
        pdb=" CZ2 TRP B 861 "   -0.003 2.00e-02 2.50e+03
        pdb=" CZ3 TRP B 861 "   -0.002 2.00e-02 2.50e+03
        pdb=" CH2 TRP B 861 "    0.003 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A 224 "   -0.029 2.00e-02 2.50e+03   2.46e-02 1.06e+01
        pdb=" CG  PHE A 224 "    0.057 2.00e-02 2.50e+03
        pdb=" CD1 PHE A 224 "   -0.009 2.00e-02 2.50e+03
        pdb=" CD2 PHE A 224 "   -0.006 2.00e-02 2.50e+03
        pdb=" CE1 PHE A 224 "   -0.003 2.00e-02 2.50e+03
        pdb=" CE2 PHE A 224 "   -0.005 2.00e-02 2.50e+03
        pdb=" CZ  PHE A 224 "   -0.006 2.00e-02 2.50e+03
  ... (remaining 2919 not shown)

  Histogram of nonbonded interaction distances:
        2.10 -     2.66: 419
        2.66 -     3.22: 17850
        3.22 -     3.78: 26730
        3.78 -     4.34: 35203
        4.34 -     4.90: 53330
  Nonbonded interactions: 133532
  Sorted by model distance:
  nonbonded pdb=" O   LYS B 488 "
            pdb=" OG  SER B 491 "
     model   vdw
     2.099 3.040
  nonbonded pdb=" O   LYS A 488 "
            pdb=" OG  SER A 491 "
     model   vdw
     2.100 3.040
  nonbonded pdb=" O   ASN A 434 "
            pdb=" OG  SER A 437 "
     model   vdw
     2.127 3.040
  nonbonded pdb=" O   ASN B 434 "
            pdb=" OG  SER B 437 "
     model   vdw
     2.128 3.040
  nonbonded pdb=" NH1 ARG A1018 "
            pdb=" OE1 GLN A1022 "
     model   vdw
     2.134 3.120
  ... (remaining 133527 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: 0.08
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

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:             4.470
  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:             0.020
  Extract box with map and model:          0.700
  Check model and map are aligned:         0.130
  Set scattering table:                    0.160
  Process input model:                     36.130
  Find NCS groups from input model:        0.280
  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:             0.010
  Load rotamer database and sin/cos tables:2.650
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   44.610
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7153
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      :  0.008   0.094  16386  Z= 0.365
  Angle     :  0.840   8.622  22244  Z= 0.472
  Chirality :  0.048   0.209   2442
  Planarity :  0.005   0.052   2922
  Dihedral  : 13.813  82.072   6070
  Min Nonbonded Distance : 2.099

Molprobity Statistics.
  All-atom Clashscore : 22.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.64 %
    Favored  : 92.36 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.64 %
    Favored  : 99.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.89 %
    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: -1.40 (0.19), residues: 2030
  helix: -0.42 (0.14), residues: 1236
  sheet: -2.24 (0.36), residues: 194
  loop : -1.19 (0.29), residues: 600

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.073   0.003   TRP A 861 
 HIS   0.007   0.002   HIS A 212 
 PHE   0.057   0.003   PHE A 224 
 TYR   0.046   0.003   TYR B1020 
 ARG   0.005   0.001   ARG A  69 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.17721 (  892)
  hydrogen bonds       : angle       7.80471 ( 2568)
  covalent geometry    : bond        0.00799 (16386)
  covalent geometry    : angle       0.83990 (22244)

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

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

  4060 Ramachandran restraints generated.
    2030 Oldfield, 0 Emsley, 2030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4060 Ramachandran restraints generated.
    2030 Oldfield, 0 Emsley, 2030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 1710 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 143
  time to evaluate  : 1.934 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   25 MET cc_start: 0.5464 (ppp) cc_final: 0.4989 (ppp)
REVERT: B   25 MET cc_start: 0.5433 (ppp) cc_final: 0.4972 (ppp)
  outliers start: 0
  outliers final: 0
  residues processed: 143
  average time/residue: 0.2493
  time to fit residues: 56.0051
Evaluate side-chains
  107 residues out of total 1710 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 107
  time to evaluate  : 1.650 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 202
   random chunks:
   chunk 170 optimal weight:    8.9990
   chunk 153 optimal weight:    8.9990
   chunk 84 optimal weight:    0.6980
   chunk 52 optimal weight:    2.9990
   chunk 103 optimal weight:    7.9990
   chunk 81 optimal weight:    9.9990
   chunk 158 optimal weight:    8.9990
   chunk 61 optimal weight:   10.0000
   chunk 96 optimal weight:    2.9990
   chunk 117 optimal weight:    1.9990
   chunk 183 optimal weight:    0.7980
   overall best weight:    1.8986

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

Flipped N/Q/H residues before XYZ refinement:
** A  84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 298 ASN
** A 581 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 629 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 834 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 859 GLN
A 928 ASN
** B  84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  97 ASN
** B 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 298 ASN
** B 581 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 629 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 814 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 834 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 859 GLN
B 928 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4236 r_free = 0.4236 target = 0.129689 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3955 r_free = 0.3955 target = 0.111939 restraints weight = 46103.065|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3923 r_free = 0.3923 target = 0.109748 restraints weight = 52473.268|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3858 r_free = 0.3858 target = 0.105970 restraints weight = 46202.083|
|-----------------------------------------------------------------------------|
r_work (final): 0.3911
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7178
moved from start:          0.1395

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.040  16386  Z= 0.205
  Angle     :  0.727   9.632  22244  Z= 0.378
  Chirality :  0.045   0.165   2442
  Planarity :  0.006   0.079   2922
  Dihedral  :  5.466  26.325   2210
  Min Nonbonded Distance : 2.438

Molprobity Statistics.
  All-atom Clashscore : 13.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.88 %
    Favored  : 95.12 %
  Rotamer:
    Outliers :  1.05 %
    Allowed  : 11.12 %
    Favored  : 87.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.89 %
    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: -0.79 (0.19), residues: 2030
  helix:  0.10 (0.14), residues: 1238
  sheet: -2.13 (0.38), residues: 166
  loop : -1.08 (0.29), residues: 626

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.045   0.002   TRP B 861 
 HIS   0.008   0.001   HIS B  65 
 PHE   0.041   0.003   PHE A  66 
 TYR   0.053   0.002   TYR A1020 
 ARG   0.017   0.001   ARG B 792 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05663 (  892)
  hydrogen bonds       : angle       5.85850 ( 2568)
  covalent geometry    : bond        0.00461 (16386)
  covalent geometry    : angle       0.72665 (22244)

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

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

  4060 Ramachandran restraints generated.
    2030 Oldfield, 0 Emsley, 2030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4060 Ramachandran restraints generated.
    2030 Oldfield, 0 Emsley, 2030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 1710 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 129
  time to evaluate  : 1.667 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  891 GLN cc_start: 0.7734 (OUTLIER) cc_final: 0.7384 (pm20)
REVERT: B  891 GLN cc_start: 0.7749 (OUTLIER) cc_final: 0.7356 (pm20)
  outliers start: 18
  outliers final: 9
  residues processed: 139
  average time/residue: 0.2734
  time to fit residues: 59.4075
Evaluate side-chains
  127 residues out of total 1710 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 116
  time to evaluate  : 1.842 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  735 VAL
Chi-restraints excluded: chain A residue  745 LEU
Chi-restraints excluded: chain A residue  858 LEU
Chi-restraints excluded: chain A residue  891 GLN
Chi-restraints excluded: chain A residue  983 LEU
Chi-restraints excluded: chain A residue 1020 TYR
Chi-restraints excluded: chain B residue  745 LEU
Chi-restraints excluded: chain B residue  858 LEU
Chi-restraints excluded: chain B residue  891 GLN
Chi-restraints excluded: chain B residue  983 LEU
Chi-restraints excluded: chain B residue 1020 TYR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 202
   random chunks:
   chunk 139 optimal weight:    0.9990
   chunk 89 optimal weight:    9.9990
   chunk 57 optimal weight:    4.9990
   chunk 3 optimal weight:    0.9990
   chunk 173 optimal weight:   20.0000
   chunk 100 optimal weight:    5.9990
   chunk 2 optimal weight:    6.9990
   chunk 95 optimal weight:    5.9990
   chunk 151 optimal weight:    0.9990
   chunk 109 optimal weight:    7.9990
   chunk 77 optimal weight:    9.9990
   overall best weight:    2.7990

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

Flipped N/Q/H residues before XYZ refinement:
A  29 HIS
** A  84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 298 ASN
** A 581 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 629 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 834 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  29 HIS
** B  84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 298 ASN
** B 581 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 629 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 834 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 863 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4214 r_free = 0.4214 target = 0.128531 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3936 r_free = 0.3936 target = 0.110946 restraints weight = 45850.765|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3877 r_free = 0.3877 target = 0.107019 restraints weight = 52261.736|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3835 r_free = 0.3835 target = 0.104752 restraints weight = 53213.527|
|-----------------------------------------------------------------------------|
r_work (final): 0.3829
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7232
moved from start:          0.1708

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.063  16386  Z= 0.263
  Angle     :  0.725  10.721  22244  Z= 0.376
  Chirality :  0.045   0.191   2442
  Planarity :  0.005   0.048   2922
  Dihedral  :  5.446  28.618   2210
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 14.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.52 %
    Favored  : 94.48 %
  Rotamer:
    Outliers :  1.93 %
    Allowed  : 15.22 %
    Favored  : 82.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.89 %
    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: -0.76 (0.19), residues: 2030
  helix:  0.20 (0.14), residues: 1240
  sheet: -2.44 (0.38), residues: 154
  loop : -1.18 (0.28), residues: 636

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.002   TRP B 861 
 HIS   0.006   0.001   HIS A 111 
 PHE   0.039   0.002   PHE A 224 
 TYR   0.058   0.002   TYR B1020 
 ARG   0.004   0.000   ARG A1018 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05449 (  892)
  hydrogen bonds       : angle       5.63211 ( 2568)
  covalent geometry    : bond        0.00595 (16386)
  covalent geometry    : angle       0.72505 (22244)

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

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

  4060 Ramachandran restraints generated.
    2030 Oldfield, 0 Emsley, 2030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4060 Ramachandran restraints generated.
    2030 Oldfield, 0 Emsley, 2030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 1710 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 127
  time to evaluate  : 1.772 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  146 TYR cc_start: 0.9078 (OUTLIER) cc_final: 0.8720 (m-10)
REVERT: A  891 GLN cc_start: 0.7773 (OUTLIER) cc_final: 0.7377 (pm20)
REVERT: B  146 TYR cc_start: 0.9080 (OUTLIER) cc_final: 0.8724 (m-10)
REVERT: B  891 GLN cc_start: 0.7753 (OUTLIER) cc_final: 0.7366 (pm20)
  outliers start: 33
  outliers final: 15
  residues processed: 150
  average time/residue: 0.2267
  time to fit residues: 55.2058
Evaluate side-chains
  138 residues out of total 1710 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 119
  time to evaluate  : 2.039 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  146 TYR
Chi-restraints excluded: chain A residue  245 VAL
Chi-restraints excluded: chain A residue  525 GLU
Chi-restraints excluded: chain A residue  637 VAL
Chi-restraints excluded: chain A residue  745 LEU
Chi-restraints excluded: chain A residue  776 VAL
Chi-restraints excluded: chain A residue  788 GLU
Chi-restraints excluded: chain A residue  858 LEU
Chi-restraints excluded: chain A residue  891 GLN
Chi-restraints excluded: chain B residue  146 TYR
Chi-restraints excluded: chain B residue  245 VAL
Chi-restraints excluded: chain B residue  525 GLU
Chi-restraints excluded: chain B residue  637 VAL
Chi-restraints excluded: chain B residue  735 VAL
Chi-restraints excluded: chain B residue  745 LEU
Chi-restraints excluded: chain B residue  776 VAL
Chi-restraints excluded: chain B residue  788 GLU
Chi-restraints excluded: chain B residue  858 LEU
Chi-restraints excluded: chain B residue  891 GLN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 202
   random chunks:
   chunk 23 optimal weight:    0.9990
   chunk 100 optimal weight:   10.0000
   chunk 118 optimal weight:    0.5980
   chunk 9 optimal weight:    5.9990
   chunk 63 optimal weight:    0.0470
   chunk 61 optimal weight:    7.9990
   chunk 73 optimal weight:    5.9990
   chunk 160 optimal weight:    0.5980
   chunk 38 optimal weight:    7.9990
   chunk 29 optimal weight:    2.9990
   chunk 20 optimal weight:    0.7980
   overall best weight:    0.6080

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

Flipped N/Q/H residues before XYZ refinement:
** A  84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 581 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 629 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 630 GLN
** A 814 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 834 GLN
** B  84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 581 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 629 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 630 GLN
** B 814 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 834 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4257 r_free = 0.4257 target = 0.131131 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3998 r_free = 0.3998 target = 0.114470 restraints weight = 47462.955|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3934 r_free = 0.3934 target = 0.110435 restraints weight = 53918.497|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3895 r_free = 0.3895 target = 0.108089 restraints weight = 38895.916|
|-----------------------------------------------------------------------------|
r_work (final): 0.3939
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7129
moved from start:          0.2248

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  16386  Z= 0.124
  Angle     :  0.654  12.502  22244  Z= 0.325
  Chirality :  0.043   0.369   2442
  Planarity :  0.005   0.052   2922
  Dihedral  :  4.937  24.699   2210
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 11.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.29 %
    Favored  : 95.71 %
  Rotamer:
    Outliers :  2.22 %
    Allowed  : 17.10 %
    Favored  : 80.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.89 %
    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: -0.41 (0.19), residues: 2030
  helix:  0.52 (0.14), residues: 1246
  sheet: -2.38 (0.37), residues: 154
  loop : -1.13 (0.28), residues: 630

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B 861 
 HIS   0.007   0.001   HIS B 111 
 PHE   0.038   0.002   PHE A  66 
 TYR   0.020   0.001   TYR A1020 
 ARG   0.004   0.000   ARG B 627 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04164 (  892)
  hydrogen bonds       : angle       4.91592 ( 2568)
  covalent geometry    : bond        0.00270 (16386)
  covalent geometry    : angle       0.65414 (22244)

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

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

  4060 Ramachandran restraints generated.
    2030 Oldfield, 0 Emsley, 2030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4060 Ramachandran restraints generated.
    2030 Oldfield, 0 Emsley, 2030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  170 residues out of total 1710 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 132
  time to evaluate  : 1.659 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  146 TYR cc_start: 0.9031 (OUTLIER) cc_final: 0.8584 (m-10)
REVERT: A  860 MET cc_start: 0.7992 (mtp) cc_final: 0.7515 (ttm)
REVERT: A  891 GLN cc_start: 0.7637 (OUTLIER) cc_final: 0.7333 (pm20)
REVERT: B  146 TYR cc_start: 0.9033 (OUTLIER) cc_final: 0.8592 (m-10)
REVERT: B  861 TRP cc_start: 0.8356 (m-90) cc_final: 0.7287 (m-90)
REVERT: B  891 GLN cc_start: 0.7649 (OUTLIER) cc_final: 0.7347 (pm20)
REVERT: B 1016 LEU cc_start: 0.8470 (pp) cc_final: 0.8167 (pp)
  outliers start: 38
  outliers final: 14
  residues processed: 162
  average time/residue: 0.2377
  time to fit residues: 60.7722
Evaluate side-chains
  137 residues out of total 1710 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 119
  time to evaluate  : 1.648 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  146 TYR
Chi-restraints excluded: chain A residue  190 PHE
Chi-restraints excluded: chain A residue  245 VAL
Chi-restraints excluded: chain A residue  533 ASP
Chi-restraints excluded: chain A residue  605 VAL
Chi-restraints excluded: chain A residue  735 VAL
Chi-restraints excluded: chain A residue  745 LEU
Chi-restraints excluded: chain A residue  788 GLU
Chi-restraints excluded: chain A residue  891 GLN
Chi-restraints excluded: chain B residue  146 TYR
Chi-restraints excluded: chain B residue  190 PHE
Chi-restraints excluded: chain B residue  245 VAL
Chi-restraints excluded: chain B residue  533 ASP
Chi-restraints excluded: chain B residue  605 VAL
Chi-restraints excluded: chain B residue  735 VAL
Chi-restraints excluded: chain B residue  745 LEU
Chi-restraints excluded: chain B residue  788 GLU
Chi-restraints excluded: chain B residue  891 GLN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 202
   random chunks:
   chunk 162 optimal weight:    4.9990
   chunk 83 optimal weight:    4.9990
   chunk 135 optimal weight:    0.9980
   chunk 125 optimal weight:    0.0470
   chunk 169 optimal weight:   10.0000
   chunk 89 optimal weight:    0.9990
   chunk 163 optimal weight:    3.9990
   chunk 121 optimal weight:    0.8980
   chunk 49 optimal weight:    3.9990
   chunk 185 optimal weight:    0.7980
   chunk 192 optimal weight:    1.9990
   overall best weight:    0.7480

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

Flipped N/Q/H residues before XYZ refinement:
** A  84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 581 HIS
** A 629 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 814 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 581 HIS
** B 629 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 814 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 834 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4260 r_free = 0.4260 target = 0.131335 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.4000 r_free = 0.4000 target = 0.114719 restraints weight = 48096.758|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3938 r_free = 0.3938 target = 0.110729 restraints weight = 51795.611|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3892 r_free = 0.3892 target = 0.107885 restraints weight = 39159.667|
|-----------------------------------------------------------------------------|
r_work (final): 0.3877
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7151
moved from start:          0.2572

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  16386  Z= 0.128
  Angle     :  0.645  11.388  22244  Z= 0.321
  Chirality :  0.042   0.145   2442
  Planarity :  0.005   0.054   2922
  Dihedral  :  4.814  23.709   2210
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 11.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.04 %
    Favored  : 95.96 %
  Rotamer:
    Outliers :  2.28 %
    Allowed  : 19.09 %
    Favored  : 78.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.89 %
    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: -0.23 (0.19), residues: 2030
  helix:  0.68 (0.15), residues: 1242
  sheet: -2.24 (0.37), residues: 164
  loop : -1.10 (0.27), residues: 624

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 861 
 HIS   0.007   0.001   HIS B 111 
 PHE   0.039   0.002   PHE B  66 
 TYR   0.019   0.001   TYR B1020 
 ARG   0.004   0.000   ARG A 913 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03996 (  892)
  hydrogen bonds       : angle       4.74866 ( 2568)
  covalent geometry    : bond        0.00288 (16386)
  covalent geometry    : angle       0.64529 (22244)

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

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

  4060 Ramachandran restraints generated.
    2030 Oldfield, 0 Emsley, 2030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4060 Ramachandran restraints generated.
    2030 Oldfield, 0 Emsley, 2030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 1710 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 128
  time to evaluate  : 1.787 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  146 TYR cc_start: 0.9035 (OUTLIER) cc_final: 0.8469 (m-10)
REVERT: A  891 GLN cc_start: 0.7714 (OUTLIER) cc_final: 0.7420 (pm20)
REVERT: B  146 TYR cc_start: 0.9028 (OUTLIER) cc_final: 0.8554 (m-10)
REVERT: B  860 MET cc_start: 0.7993 (mtp) cc_final: 0.7713 (ttm)
REVERT: B  891 GLN cc_start: 0.7702 (OUTLIER) cc_final: 0.7401 (pm20)
  outliers start: 39
  outliers final: 16
  residues processed: 163
  average time/residue: 0.2415
  time to fit residues: 62.9209
Evaluate side-chains
  132 residues out of total 1710 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 112
  time to evaluate  : 1.678 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  146 TYR
Chi-restraints excluded: chain A residue  190 PHE
Chi-restraints excluded: chain A residue  245 VAL
Chi-restraints excluded: chain A residue  533 ASP
Chi-restraints excluded: chain A residue  653 LEU
Chi-restraints excluded: chain A residue  735 VAL
Chi-restraints excluded: chain A residue  745 LEU
Chi-restraints excluded: chain A residue  776 VAL
Chi-restraints excluded: chain A residue  788 GLU
Chi-restraints excluded: chain A residue  891 GLN
Chi-restraints excluded: chain B residue  146 TYR
Chi-restraints excluded: chain B residue  190 PHE
Chi-restraints excluded: chain B residue  245 VAL
Chi-restraints excluded: chain B residue  533 ASP
Chi-restraints excluded: chain B residue  653 LEU
Chi-restraints excluded: chain B residue  735 VAL
Chi-restraints excluded: chain B residue  745 LEU
Chi-restraints excluded: chain B residue  776 VAL
Chi-restraints excluded: chain B residue  788 GLU
Chi-restraints excluded: chain B residue  891 GLN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 202
   random chunks:
   chunk 104 optimal weight:    8.9990
   chunk 97 optimal weight:    1.9990
   chunk 82 optimal weight:    0.9980
   chunk 58 optimal weight:    7.9990
   chunk 64 optimal weight:    6.9990
   chunk 176 optimal weight:    3.9990
   chunk 66 optimal weight:    3.9990
   chunk 94 optimal weight:    5.9990
   chunk 31 optimal weight:    0.9980
   chunk 197 optimal weight:    0.8980
   chunk 119 optimal weight:    0.9980
   overall best weight:    1.1782

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

Flipped N/Q/H residues before XYZ refinement:
** A  84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 629 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 814 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 629 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 814 ASN ** 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 = 0.4251 r_free = 0.4251 target = 0.130751 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3989 r_free = 0.3989 target = 0.114158 restraints weight = 47721.656|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3926 r_free = 0.3926 target = 0.110242 restraints weight = 53489.059|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3887 r_free = 0.3887 target = 0.107875 restraints weight = 43314.498|
|-----------------------------------------------------------------------------|
r_work (final): 0.3878
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7153
moved from start:          0.2715

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  16386  Z= 0.143
  Angle     :  0.654  11.751  22244  Z= 0.326
  Chirality :  0.042   0.151   2442
  Planarity :  0.005   0.052   2922
  Dihedral  :  4.733  23.064   2210
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 11.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.29 %
    Favored  : 95.71 %
  Rotamer:
    Outliers :  2.05 %
    Allowed  : 19.73 %
    Favored  : 78.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.89 %
    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: -0.00 (0.19), residues: 2030
  helix:  0.85 (0.15), residues: 1232
  sheet: -2.10 (0.39), residues: 152
  loop : -0.99 (0.27), residues: 646

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 861 
 HIS   0.007   0.001   HIS B 111 
 PHE   0.039   0.002   PHE B  66 
 TYR   0.018   0.001   TYR A1020 
 ARG   0.003   0.000   ARG B 913 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03975 (  892)
  hydrogen bonds       : angle       4.74620 ( 2568)
  covalent geometry    : bond        0.00328 (16386)
  covalent geometry    : angle       0.65397 (22244)

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

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

  4060 Ramachandran restraints generated.
    2030 Oldfield, 0 Emsley, 2030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4060 Ramachandran restraints generated.
    2030 Oldfield, 0 Emsley, 2030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 1710 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 128
  time to evaluate  : 1.827 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  146 TYR cc_start: 0.9120 (OUTLIER) cc_final: 0.8564 (m-10)
REVERT: A  860 MET cc_start: 0.7998 (mtp) cc_final: 0.7687 (ttm)
REVERT: A  891 GLN cc_start: 0.7712 (OUTLIER) cc_final: 0.7398 (pm20)
REVERT: A  946 MET cc_start: 0.7990 (ppp) cc_final: 0.7634 (ptp)
REVERT: B  146 TYR cc_start: 0.9117 (OUTLIER) cc_final: 0.8558 (m-10)
REVERT: B  860 MET cc_start: 0.8032 (mtp) cc_final: 0.7720 (ttm)
REVERT: B  891 GLN cc_start: 0.7690 (OUTLIER) cc_final: 0.7369 (pm20)
REVERT: B  946 MET cc_start: 0.7997 (ppp) cc_final: 0.7657 (ptp)
REVERT: B 1016 LEU cc_start: 0.8630 (pp) cc_final: 0.8285 (pp)
  outliers start: 35
  outliers final: 21
  residues processed: 157
  average time/residue: 0.2307
  time to fit residues: 58.7275
Evaluate side-chains
  146 residues out of total 1710 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 121
  time to evaluate  : 1.650 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  146 TYR
Chi-restraints excluded: chain A residue  190 PHE
Chi-restraints excluded: chain A residue  192 VAL
Chi-restraints excluded: chain A residue  245 VAL
Chi-restraints excluded: chain A residue  533 ASP
Chi-restraints excluded: chain A residue  653 LEU
Chi-restraints excluded: chain A residue  741 LEU
Chi-restraints excluded: chain A residue  745 LEU
Chi-restraints excluded: chain A residue  776 VAL
Chi-restraints excluded: chain A residue  788 GLU
Chi-restraints excluded: chain A residue  858 LEU
Chi-restraints excluded: chain A residue  891 GLN
Chi-restraints excluded: chain B residue  146 TYR
Chi-restraints excluded: chain B residue  190 PHE
Chi-restraints excluded: chain B residue  192 VAL
Chi-restraints excluded: chain B residue  245 VAL
Chi-restraints excluded: chain B residue  533 ASP
Chi-restraints excluded: chain B residue  653 LEU
Chi-restraints excluded: chain B residue  735 VAL
Chi-restraints excluded: chain B residue  741 LEU
Chi-restraints excluded: chain B residue  745 LEU
Chi-restraints excluded: chain B residue  776 VAL
Chi-restraints excluded: chain B residue  788 GLU
Chi-restraints excluded: chain B residue  858 LEU
Chi-restraints excluded: chain B residue  891 GLN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 202
   random chunks:
   chunk 188 optimal weight:   10.0000
   chunk 67 optimal weight:    5.9990
   chunk 10 optimal weight:    0.9990
   chunk 3 optimal weight:    9.9990
   chunk 44 optimal weight:    0.8980
   chunk 26 optimal weight:    1.9990
   chunk 182 optimal weight:   10.0000
   chunk 93 optimal weight:    8.9990
   chunk 85 optimal weight:    3.9990
   chunk 196 optimal weight:    1.9990
   chunk 14 optimal weight:    0.8980
   overall best weight:    1.3586

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

Flipped N/Q/H residues before XYZ refinement:
** A  65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 629 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 814 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 629 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 814 ASN ** 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 = 0.4248 r_free = 0.4248 target = 0.130604 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3991 r_free = 0.3991 target = 0.114245 restraints weight = 47813.175|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3929 r_free = 0.3929 target = 0.110395 restraints weight = 51673.755|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3883 r_free = 0.3883 target = 0.107586 restraints weight = 39809.946|
|-----------------------------------------------------------------------------|
r_work (final): 0.3930
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7148
moved from start:          0.2840

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032  16386  Z= 0.153
  Angle     :  0.671  11.185  22244  Z= 0.331
  Chirality :  0.043   0.222   2442
  Planarity :  0.005   0.055   2922
  Dihedral  :  4.711  22.706   2210
  Min Nonbonded Distance : 2.552

Molprobity Statistics.
  All-atom Clashscore : 11.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.38 %
    Favored  : 95.62 %
  Rotamer:
    Outliers :  2.69 %
    Allowed  : 20.61 %
    Favored  : 76.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.89 %
    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:  0.04 (0.19), residues: 2030
  helix:  0.87 (0.15), residues: 1232
  sheet: -2.17 (0.38), residues: 154
  loop : -0.90 (0.27), residues: 644

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 861 
 HIS   0.007   0.001   HIS B 111 
 PHE   0.042   0.002   PHE A  66 
 TYR   0.045   0.001   TYR A1020 
 ARG   0.003   0.000   ARG A  69 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03958 (  892)
  hydrogen bonds       : angle       4.75658 ( 2568)
  covalent geometry    : bond        0.00351 (16386)
  covalent geometry    : angle       0.67135 (22244)

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

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

  4060 Ramachandran restraints generated.
    2030 Oldfield, 0 Emsley, 2030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4060 Ramachandran restraints generated.
    2030 Oldfield, 0 Emsley, 2030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 1710 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 126
  time to evaluate  : 1.748 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  146 TYR cc_start: 0.9089 (OUTLIER) cc_final: 0.8476 (m-10)
REVERT: A  860 MET cc_start: 0.7898 (mtp) cc_final: 0.7591 (ttm)
REVERT: A  891 GLN cc_start: 0.7663 (OUTLIER) cc_final: 0.7392 (pm20)
REVERT: B  146 TYR cc_start: 0.9084 (OUTLIER) cc_final: 0.8502 (m-10)
REVERT: B  860 MET cc_start: 0.7919 (mtp) cc_final: 0.7595 (ttm)
REVERT: B  891 GLN cc_start: 0.7623 (OUTLIER) cc_final: 0.7337 (pm20)
  outliers start: 46
  outliers final: 26
  residues processed: 168
  average time/residue: 0.2191
  time to fit residues: 60.0720
Evaluate side-chains
  154 residues out of total 1710 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 124
  time to evaluate  : 1.818 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   55 THR
Chi-restraints excluded: chain A residue  146 TYR
Chi-restraints excluded: chain A residue  190 PHE
Chi-restraints excluded: chain A residue  192 VAL
Chi-restraints excluded: chain A residue  240 ILE
Chi-restraints excluded: chain A residue  245 VAL
Chi-restraints excluded: chain A residue  533 ASP
Chi-restraints excluded: chain A residue  653 LEU
Chi-restraints excluded: chain A residue  741 LEU
Chi-restraints excluded: chain A residue  745 LEU
Chi-restraints excluded: chain A residue  776 VAL
Chi-restraints excluded: chain A residue  782 ILE
Chi-restraints excluded: chain A residue  788 GLU
Chi-restraints excluded: chain A residue  891 GLN
Chi-restraints excluded: chain A residue  927 CYS
Chi-restraints excluded: chain B residue   55 THR
Chi-restraints excluded: chain B residue  146 TYR
Chi-restraints excluded: chain B residue  190 PHE
Chi-restraints excluded: chain B residue  192 VAL
Chi-restraints excluded: chain B residue  240 ILE
Chi-restraints excluded: chain B residue  245 VAL
Chi-restraints excluded: chain B residue  533 ASP
Chi-restraints excluded: chain B residue  653 LEU
Chi-restraints excluded: chain B residue  741 LEU
Chi-restraints excluded: chain B residue  745 LEU
Chi-restraints excluded: chain B residue  776 VAL
Chi-restraints excluded: chain B residue  788 GLU
Chi-restraints excluded: chain B residue  858 LEU
Chi-restraints excluded: chain B residue  891 GLN
Chi-restraints excluded: chain B residue  927 CYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 202
   random chunks:
   chunk 95 optimal weight:    0.9990
   chunk 166 optimal weight:    4.9990
   chunk 159 optimal weight:    7.9990
   chunk 81 optimal weight:    0.9980
   chunk 16 optimal weight:    0.5980
   chunk 171 optimal weight:   20.0000
   chunk 96 optimal weight:    1.9990
   chunk 8 optimal weight:    4.9990
   chunk 26 optimal weight:    1.9990
   chunk 37 optimal weight:    3.9990
   chunk 175 optimal weight:    2.9990
   overall best weight:    1.3186

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

Flipped N/Q/H residues before XYZ refinement:
** A  65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 629 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 814 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 629 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 806 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 814 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 834 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 = 0.4252 r_free = 0.4252 target = 0.130817 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3992 r_free = 0.3992 target = 0.114285 restraints weight = 47256.945|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3931 r_free = 0.3931 target = 0.110553 restraints weight = 52317.505|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3884 r_free = 0.3884 target = 0.107623 restraints weight = 44533.545|
|-----------------------------------------------------------------------------|
r_work (final): 0.3868
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7161
moved from start:          0.2988

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  16386  Z= 0.152
  Angle     :  0.693  13.371  22244  Z= 0.340
  Chirality :  0.043   0.229   2442
  Planarity :  0.005   0.054   2922
  Dihedral  :  4.673  22.599   2210
  Min Nonbonded Distance : 2.552

Molprobity Statistics.
  All-atom Clashscore : 11.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.58 %
    Favored  : 95.42 %
  Rotamer:
    Outliers :  2.34 %
    Allowed  : 21.25 %
    Favored  : 76.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.89 %
    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:  0.09 (0.19), residues: 2030
  helix:  0.90 (0.15), residues: 1234
  sheet: -2.15 (0.37), residues: 164
  loop : -0.84 (0.28), residues: 632

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.035   0.002   TRP B  48 
 HIS   0.007   0.001   HIS B 111 
 PHE   0.042   0.002   PHE A  66 
 TYR   0.011   0.001   TYR A1020 
 ARG   0.003   0.000   ARG A1018 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03931 (  892)
  hydrogen bonds       : angle       4.74378 ( 2568)
  covalent geometry    : bond        0.00350 (16386)
  covalent geometry    : angle       0.69317 (22244)

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

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

  4060 Ramachandran restraints generated.
    2030 Oldfield, 0 Emsley, 2030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4060 Ramachandran restraints generated.
    2030 Oldfield, 0 Emsley, 2030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 1710 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 129
  time to evaluate  : 2.607 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   25 MET cc_start: 0.4377 (ppp) cc_final: 0.3872 (ppp)
REVERT: A  146 TYR cc_start: 0.9092 (OUTLIER) cc_final: 0.8600 (m-10)
REVERT: A  860 MET cc_start: 0.8088 (mtp) cc_final: 0.7803 (ttm)
REVERT: A  891 GLN cc_start: 0.7724 (OUTLIER) cc_final: 0.7423 (pm20)
REVERT: B   25 MET cc_start: 0.4364 (ppp) cc_final: 0.3914 (ppp)
REVERT: B  146 TYR cc_start: 0.9091 (OUTLIER) cc_final: 0.8598 (m-10)
REVERT: B  860 MET cc_start: 0.8114 (mtp) cc_final: 0.7860 (ttm)
REVERT: B  891 GLN cc_start: 0.7683 (OUTLIER) cc_final: 0.7371 (pm20)
REVERT: B 1016 LEU cc_start: 0.8718 (pp) cc_final: 0.8423 (pp)
  outliers start: 40
  outliers final: 26
  residues processed: 163
  average time/residue: 0.2338
  time to fit residues: 62.1570
Evaluate side-chains
  153 residues out of total 1710 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 123
  time to evaluate  : 1.906 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   55 THR
Chi-restraints excluded: chain A residue  146 TYR
Chi-restraints excluded: chain A residue  190 PHE
Chi-restraints excluded: chain A residue  192 VAL
Chi-restraints excluded: chain A residue  240 ILE
Chi-restraints excluded: chain A residue  245 VAL
Chi-restraints excluded: chain A residue  533 ASP
Chi-restraints excluded: chain A residue  653 LEU
Chi-restraints excluded: chain A residue  741 LEU
Chi-restraints excluded: chain A residue  745 LEU
Chi-restraints excluded: chain A residue  776 VAL
Chi-restraints excluded: chain A residue  788 GLU
Chi-restraints excluded: chain A residue  795 ILE
Chi-restraints excluded: chain A residue  858 LEU
Chi-restraints excluded: chain A residue  891 GLN
Chi-restraints excluded: chain B residue   55 THR
Chi-restraints excluded: chain B residue  146 TYR
Chi-restraints excluded: chain B residue  190 PHE
Chi-restraints excluded: chain B residue  192 VAL
Chi-restraints excluded: chain B residue  240 ILE
Chi-restraints excluded: chain B residue  245 VAL
Chi-restraints excluded: chain B residue  533 ASP
Chi-restraints excluded: chain B residue  653 LEU
Chi-restraints excluded: chain B residue  741 LEU
Chi-restraints excluded: chain B residue  745 LEU
Chi-restraints excluded: chain B residue  776 VAL
Chi-restraints excluded: chain B residue  782 ILE
Chi-restraints excluded: chain B residue  788 GLU
Chi-restraints excluded: chain B residue  858 LEU
Chi-restraints excluded: chain B residue  891 GLN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 202
   random chunks:
   chunk 105 optimal weight:   10.0000
   chunk 147 optimal weight:    0.8980
   chunk 50 optimal weight:    3.9990
   chunk 98 optimal weight:    3.9990
   chunk 68 optimal weight:    4.9990
   chunk 163 optimal weight:    4.9990
   chunk 150 optimal weight:    0.9980
   chunk 28 optimal weight:    2.9990
   chunk 55 optimal weight:    5.9990
   chunk 112 optimal weight:    1.9990
   chunk 101 optimal weight:   20.0000
   overall best weight:    2.1786

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

Flipped N/Q/H residues before XYZ refinement:
** A  50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 332 ASN
** A 629 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 806 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 814 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 834 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 332 ASN
** B 629 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 806 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 834 GLN ** 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 = 0.4236 r_free = 0.4236 target = 0.129709 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3964 r_free = 0.3964 target = 0.112631 restraints weight = 47400.204|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3921 r_free = 0.3921 target = 0.109891 restraints weight = 53640.686|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3861 r_free = 0.3861 target = 0.106367 restraints weight = 48189.567|
|-----------------------------------------------------------------------------|
r_work (final): 0.3910
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7188
moved from start:          0.2948

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.051  16386  Z= 0.209
  Angle     :  0.744  13.543  22244  Z= 0.365
  Chirality :  0.045   0.221   2442
  Planarity :  0.005   0.054   2922
  Dihedral  :  4.796  24.452   2210
  Min Nonbonded Distance : 2.552

Molprobity Statistics.
  All-atom Clashscore : 12.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.58 %
    Favored  : 95.42 %
  Rotamer:
    Outliers :  1.99 %
    Allowed  : 22.01 %
    Favored  : 76.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.89 %
    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:  0.05 (0.19), residues: 2030
  helix:  0.84 (0.15), residues: 1228
  sheet: -2.15 (0.37), residues: 164
  loop : -0.78 (0.28), residues: 638

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B1024 
 HIS   0.007   0.001   HIS A  43 
 PHE   0.043   0.002   PHE A  66 
 TYR   0.034   0.001   TYR A 989 
 ARG   0.003   0.000   ARG B  69 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04347 (  892)
  hydrogen bonds       : angle       4.96627 ( 2568)
  covalent geometry    : bond        0.00483 (16386)
  covalent geometry    : angle       0.74359 (22244)

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

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

  4060 Ramachandran restraints generated.
    2030 Oldfield, 0 Emsley, 2030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4060 Ramachandran restraints generated.
    2030 Oldfield, 0 Emsley, 2030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 1710 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 125
  time to evaluate  : 1.704 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   25 MET cc_start: 0.4240 (ppp) cc_final: 0.3780 (ppp)
REVERT: A  146 TYR cc_start: 0.9103 (OUTLIER) cc_final: 0.8632 (m-10)
REVERT: A  860 MET cc_start: 0.8028 (mtp) cc_final: 0.7770 (ttm)
REVERT: A  891 GLN cc_start: 0.7705 (OUTLIER) cc_final: 0.7403 (pm20)
REVERT: A  930 HIS cc_start: 0.8183 (OUTLIER) cc_final: 0.7627 (m90)
REVERT: A  946 MET cc_start: 0.7927 (ppp) cc_final: 0.7673 (ptp)
REVERT: B   25 MET cc_start: 0.4330 (ppp) cc_final: 0.3908 (ppp)
REVERT: B  146 TYR cc_start: 0.9101 (OUTLIER) cc_final: 0.8635 (m-10)
REVERT: B  891 GLN cc_start: 0.7689 (OUTLIER) cc_final: 0.7387 (pm20)
REVERT: B  930 HIS cc_start: 0.8139 (OUTLIER) cc_final: 0.7528 (m90)
REVERT: B 1016 LEU cc_start: 0.8690 (pp) cc_final: 0.8414 (pp)
  outliers start: 34
  outliers final: 28
  residues processed: 155
  average time/residue: 0.2213
  time to fit residues: 55.5006
Evaluate side-chains
  159 residues out of total 1710 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 125
  time to evaluate  : 1.695 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   55 THR
Chi-restraints excluded: chain A residue  146 TYR
Chi-restraints excluded: chain A residue  190 PHE
Chi-restraints excluded: chain A residue  192 VAL
Chi-restraints excluded: chain A residue  240 ILE
Chi-restraints excluded: chain A residue  245 VAL
Chi-restraints excluded: chain A residue  533 ASP
Chi-restraints excluded: chain A residue  653 LEU
Chi-restraints excluded: chain A residue  741 LEU
Chi-restraints excluded: chain A residue  745 LEU
Chi-restraints excluded: chain A residue  776 VAL
Chi-restraints excluded: chain A residue  782 ILE
Chi-restraints excluded: chain A residue  788 GLU
Chi-restraints excluded: chain A residue  795 ILE
Chi-restraints excluded: chain A residue  858 LEU
Chi-restraints excluded: chain A residue  891 GLN
Chi-restraints excluded: chain A residue  930 HIS
Chi-restraints excluded: chain B residue   55 THR
Chi-restraints excluded: chain B residue  146 TYR
Chi-restraints excluded: chain B residue  190 PHE
Chi-restraints excluded: chain B residue  192 VAL
Chi-restraints excluded: chain B residue  240 ILE
Chi-restraints excluded: chain B residue  245 VAL
Chi-restraints excluded: chain B residue  533 ASP
Chi-restraints excluded: chain B residue  653 LEU
Chi-restraints excluded: chain B residue  741 LEU
Chi-restraints excluded: chain B residue  745 LEU
Chi-restraints excluded: chain B residue  776 VAL
Chi-restraints excluded: chain B residue  782 ILE
Chi-restraints excluded: chain B residue  788 GLU
Chi-restraints excluded: chain B residue  795 ILE
Chi-restraints excluded: chain B residue  858 LEU
Chi-restraints excluded: chain B residue  891 GLN
Chi-restraints excluded: chain B residue  930 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 202
   random chunks:
   chunk 105 optimal weight:   10.0000
   chunk 51 optimal weight:    0.7980
   chunk 30 optimal weight:    0.5980
   chunk 102 optimal weight:    5.9990
   chunk 62 optimal weight:    3.9990
   chunk 135 optimal weight:    0.6980
   chunk 187 optimal weight:    0.8980
   chunk 157 optimal weight:    8.9990
   chunk 73 optimal weight:    6.9990
   chunk 39 optimal weight:    2.9990
   chunk 17 optimal weight:    0.5980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
** A  50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A  84 GLN
** A 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 629 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 814 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 629 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 814 ASN ** 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 = 0.4263 r_free = 0.4263 target = 0.131440 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3996 r_free = 0.3996 target = 0.114495 restraints weight = 47863.805|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3930 r_free = 0.3930 target = 0.110338 restraints weight = 55720.290|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3885 r_free = 0.3885 target = 0.107549 restraints weight = 42959.561|
|-----------------------------------------------------------------------------|
r_work (final): 0.3867
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7166
moved from start:          0.3203

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  16386  Z= 0.128
  Angle     :  0.737  15.626  22244  Z= 0.353
  Chirality :  0.044   0.300   2442
  Planarity :  0.005   0.054   2922
  Dihedral  :  4.617  22.088   2210
  Min Nonbonded Distance : 2.552

Molprobity Statistics.
  All-atom Clashscore : 11.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.94 %
    Favored  : 96.06 %
  Rotamer:
    Outliers :  1.81 %
    Allowed  : 22.25 %
    Favored  : 75.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.89 %
    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:  0.17 (0.20), residues: 2030
  helix:  0.95 (0.15), residues: 1232
  sheet: -2.00 (0.36), residues: 174
  loop : -0.77 (0.28), residues: 624

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B1024 
 HIS   0.007   0.001   HIS B 111 
 PHE   0.045   0.002   PHE B  66 
 TYR   0.035   0.001   TYR B 989 
 ARG   0.003   0.000   ARG A  69 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03780 (  892)
  hydrogen bonds       : angle       4.74646 ( 2568)
  covalent geometry    : bond        0.00289 (16386)
  covalent geometry    : angle       0.73669 (22244)

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

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

  4060 Ramachandran restraints generated.
    2030 Oldfield, 0 Emsley, 2030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4060 Ramachandran restraints generated.
    2030 Oldfield, 0 Emsley, 2030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 1710 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 126
  time to evaluate  : 1.925 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   25 MET cc_start: 0.4385 (ppp) cc_final: 0.4007 (ppp)
REVERT: A  146 TYR cc_start: 0.9074 (OUTLIER) cc_final: 0.8491 (m-10)
REVERT: A  789 MET cc_start: 0.4795 (tmm) cc_final: 0.4556 (tmm)
REVERT: A  860 MET cc_start: 0.8050 (mtp) cc_final: 0.7838 (mtt)
REVERT: A  891 GLN cc_start: 0.7717 (OUTLIER) cc_final: 0.7479 (pm20)
REVERT: B   25 MET cc_start: 0.4484 (ppp) cc_final: 0.4091 (ppp)
REVERT: B  146 TYR cc_start: 0.9074 (OUTLIER) cc_final: 0.8496 (m-10)
REVERT: B  789 MET cc_start: 0.4744 (tmm) cc_final: 0.4504 (tmm)
REVERT: B  891 GLN cc_start: 0.7685 (OUTLIER) cc_final: 0.7440 (pm20)
REVERT: B 1016 LEU cc_start: 0.8706 (pp) cc_final: 0.8476 (pp)
  outliers start: 31
  outliers final: 24
  residues processed: 153
  average time/residue: 0.2479
  time to fit residues: 61.0940
Evaluate side-chains
  153 residues out of total 1710 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 125
  time to evaluate  : 1.849 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   55 THR
Chi-restraints excluded: chain A residue  146 TYR
Chi-restraints excluded: chain A residue  190 PHE
Chi-restraints excluded: chain A residue  192 VAL
Chi-restraints excluded: chain A residue  245 VAL
Chi-restraints excluded: chain A residue  533 ASP
Chi-restraints excluded: chain A residue  653 LEU
Chi-restraints excluded: chain A residue  741 LEU
Chi-restraints excluded: chain A residue  745 LEU
Chi-restraints excluded: chain A residue  776 VAL
Chi-restraints excluded: chain A residue  788 GLU
Chi-restraints excluded: chain A residue  891 GLN
Chi-restraints excluded: chain B residue   55 THR
Chi-restraints excluded: chain B residue  146 TYR
Chi-restraints excluded: chain B residue  190 PHE
Chi-restraints excluded: chain B residue  192 VAL
Chi-restraints excluded: chain B residue  245 VAL
Chi-restraints excluded: chain B residue  533 ASP
Chi-restraints excluded: chain B residue  653 LEU
Chi-restraints excluded: chain B residue  741 LEU
Chi-restraints excluded: chain B residue  745 LEU
Chi-restraints excluded: chain B residue  776 VAL
Chi-restraints excluded: chain B residue  782 ILE
Chi-restraints excluded: chain B residue  788 GLU
Chi-restraints excluded: chain B residue  795 ILE
Chi-restraints excluded: chain B residue  811 THR
Chi-restraints excluded: chain B residue  858 LEU
Chi-restraints excluded: chain B residue  891 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 202
   random chunks:
   chunk 6 optimal weight:    0.3980
   chunk 12 optimal weight:    0.5980
   chunk 198 optimal weight:    0.9990
   chunk 137 optimal weight:    0.7980
   chunk 155 optimal weight:    0.9980
   chunk 4 optimal weight:   10.0000
   chunk 80 optimal weight:    9.9990
   chunk 154 optimal weight:   10.0000
   chunk 181 optimal weight:    9.9990
   chunk 162 optimal weight:    7.9990
   chunk 175 optimal weight:   40.0000
   overall best weight:    0.7582

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

Flipped N/Q/H residues before XYZ refinement:
** A 629 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  84 GLN
** B 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 629 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4305 r_free = 0.4305 target = 0.133798 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.4058 r_free = 0.4058 target = 0.117912 restraints weight = 49358.257|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.4013 r_free = 0.4013 target = 0.115028 restraints weight = 56974.685|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3971 r_free = 0.3971 target = 0.112399 restraints weight = 52216.569|
|-----------------------------------------------------------------------------|
r_work (final): 0.3965
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7062
moved from start:          0.3331

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  16386  Z= 0.129
  Angle     :  0.739  14.873  22244  Z= 0.353
  Chirality :  0.044   0.321   2442
  Planarity :  0.005   0.071   2922
  Dihedral  :  4.527  21.691   2210
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 11.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.04 %
    Favored  : 95.96 %
  Rotamer:
    Outliers :  1.87 %
    Allowed  : 21.96 %
    Favored  : 76.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.89 %
    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:  0.28 (0.20), residues: 2030
  helix:  1.03 (0.15), residues: 1232
  sheet: -1.90 (0.37), residues: 174
  loop : -0.73 (0.28), residues: 624

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B1024 
 HIS   0.007   0.001   HIS A 111 
 PHE   0.045   0.002   PHE B  66 
 TYR   0.033   0.001   TYR A 989 
 ARG   0.022   0.000   ARG A 792 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03711 (  892)
  hydrogen bonds       : angle       4.73588 ( 2568)
  covalent geometry    : bond        0.00293 (16386)
  covalent geometry    : angle       0.73870 (22244)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4638.46 seconds
wall clock time: 83 minutes 0.25 seconds (4980.25 seconds total)